Re: [galaxy-dev] Settings multiple Genome Indices
There's an as-yet undocumented method that you can use to get arbitrary fields
in a loc file:
__get_data_table_entry__(table_name, key_field, field_value,
value_field)
So for the novoalign entry you could do:
--novoidx ${__get_data_table_entry__(‘novoalign’, ‘dbkey’, $input.dbkey,
‘path’)}
Finally, I like your indexing syntax, and it would be great to use something
like that in place of the explicit method call above.
Best,
J.
--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington University
On Jul 27, 2014, at 10:44 AM, Geert Vandeweyer
geert.vandewey...@uantwerpen.be wrote:
Hi,
I'm working on tool wrapper that needs three reference genome locations
(2bit/lastz, all_fasta and novoalign). Is there a way to fetch the three
paths from the loc files using a single select box? I've looked around in a
couple of tool wrappers on the toolshed, but could find any leads. Something
like the following would be ok:
Select options from all_fasta.loc
- upon change, set hidden variables to novoalign.loc + lastz_seqs.loc
using a filter tag or something against the selected options from all_fasta.
Even more simple : access in the command tag like:
--novoidx novoalign-loc.options[dbkey=$input.dbkey,path] --fasta
all_fasta-loc[dbkey=$input.dbkey,path] etc , using the dbkey from the input
file (which is a bam file in this case)
In this case, error handling should come from the tool, if one of the indices
is missing.
I'm currently using three selection boxes, but that looks a but redundant to
the user, as they all have to select the same thing.
Best,
Geert
--
Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer
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Re: [galaxy-dev] Trackster : Error visualising VCF
This is due to a mismatch is chromosome names between your hg19.len file (UCSC naming) and the VCF (Ensembl naming). This should be handled better by Galaxy, and I’ve created a card for it: https://trello.com/c/bjmNesZj In the meantime, I used this command to convert chromosome names for this VCF: sed -E 's/^[0-9XY]+/chr/‘ input.vcf | sed -E 's/^MT/chrM/' You may need to massage it depending on your platform and sed version. Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Apr 20, 2014, at 11:27 AM, Saket Choudhary sake...@gmail.com wrote: I am trying to visualise VCF exported from: ftp://ngs.sanger.ac.uk/production/cosmic/CosmicCodingMuts_v68.vcf.gz However I get the following error: (Both on Galaxy Main and Local installation) Input error: Chromosome 1 found in your input file but not in your genome file. needLargeMem: trying to allocate 0 bytes (limit: 1000) The input file seems to be conforming to VCF4.1 format. Is this an issue with trackster instead? Saket ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Trackster shared Visualization in an iframe
This is a good idea, and I’ve implemented it in this -central changeset: https://bitbucket.org/galaxy/galaxy-central/commits/c055181847a46dc3199458d899d28d559ae43c38 If you’re working with galaxy-dist, you can pull this one changeset and use it until the next release. Let me know if you have any problems. Best, J. On Apr 17, 2014, at 6:52 AM, Raphael Müller raphael.muel...@mni.thm.de wrote: Hello, I am developing a web application, where I want to show a Trackster visualization in an iframe from our local Galaxy Server. The problem is that I am not able to specify over a locus via the URL when I am not the owner of the visualization. (When we click saved Visualization we can specify the region via the link to the visualization, we can call e.g. .../visualization/trackster?id=1cd8e2f6b131e891#chr19:1234-5678.) Is there any possibility to show a shared visualization in an iframe at a specific locus? Greetings Raphael Müller ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Problem upgrading bx-python to fix trackster error.
Hi Will, This should be fixed as of this commit: https://bitbucket.org/galaxy/galaxy-central/commits/3a154b52090316dee61f42993eaa5a1fa40116d3 Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Apr 9, 2014, at 10:03 PM, William Holtz who...@lygos.com wrote: I have a set of galaxy generated bam and bigwig files containing over 600 contigs. When I attempt to view any of these files with trackster (on a local server running current galaxy-dist) I get the following in my log file: galaxy.webapps.galaxy.api.datasets ERROR 2014-04-09 17:41:16,063 Error in dataset API at listing contents: 'BinaryFileReader' object has no attribute 'read_bits64': 'BinaryFileReader' object has no attribute 'read_bits64' Traceback (most recent call last): File /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py, line 44, in show is_true( kwd.get( 'retry', False ) ) ) File /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py, line 106, in _converted_datasets_state if not data_provider.has_data( chrom ): File /home/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py, line 1078, in has_data all_dat = bbi.query( chrom, 0, 2147483647, 1 ) or \ File bbi_file.pyx, line 215, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5596) File bbi_file.pyx, line 222, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5210) File bbi_file.pyx, line 183, in bx.bbi.bbi_file.BBIFile.summarize (lib/bx/bbi/bbi_file.c:4475) File bbi_file.pyx, line 248, in bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size (lib/bx/bbi/bbi_file.c:5656) File bpt_file.pyx, line 76, in bx.bbi.bpt_file.BPTFile.find (lib/bx/bbi/bpt_file.c:1388) File bpt_file.pyx, line 55, in bx.bbi.bpt_file.BPTFile.r_find (lib/bx/bbi/bpt_file.c:1154) AttributeError: 'BinaryFileReader' object has no attribute 'read_bits64' Two people have previously reported similar errors to this list. I don't know how to reply to messages that predate me joining the list, so here are links to the threads: http://dev.list.galaxyproject.org/read-bits64-error-when-loading-large-genomes-data-into-trackster-tp4663622.html http://dev.list.galaxyproject.org/trackster-error-for-viewing-rat-data-rn5-tp4662664.html Following the suggestion of Jeremy Goecks in one of those old threads, I checked my bx-python version. The directory name bx-python is installed in indicates that I have version 0.7.1. Version 0.7.1 is from 2011 and pre-dates the the bug Jeremy mentioned (https://bitbucket.org/james_taylor/bx-python/commits/24893a84ce13a18815e3006c9f89b3828022ac96). Additionally, I ran: strings ./galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bpt_file.so | grep read_bits64 and found a match, thus confirming the installed version pre-dates the bug fix, as all references to read_bits64 were removed in that commit. Additionally I cloned and compiled the current version of bx-python and found that the above command did not find any matches. The offending installation of bx-python is part of the base installation of galaxy and not an item I added from the toolshed. I am unsure of how to go about replacing this egg with the newer version of bx-python. If someone can update the bx-python egg on http://eggs.g2.bx.psu.edu/ or give me instructions on how to replace my copy of the egg, I would greatly appreciate it! Additionally, I found that all three of the versions of bx-python in the galaxy-main toolshed still contain this bug. Of the three versions of bx-python int the galaxy-test toolshed, only 3:5457e32b427c (2013-12-14) contains the bug fix. Thank you in advance for your assistance! -Will ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] read_bits64 error when loading large genomes/data into trackster
Hi Raj, Thanks for sharing your datasets. This issue should be fixed as of this commit in -central: https://bitbucket.org/galaxy/galaxy-central/commits/3a154b52090316dee61f42993eaa5a1fa40116d3 Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 25, 2014, at 11:15 AM, Raj Ayyampalayam ra...@uga.edu wrote: Jeremy, I uploaded my dataset to the main galaxy site and the visualization failed. Here is the link to the history: https://usegalaxy.org/u/raj-a-n/h/amborella-viz-test I used the same genome and a cufflinks gtf file instead of the bam file (Bam is too big to load). I am seeing the same problem on both main and my local galaxy instances (local is tracking latest galaxy-dist). Thanks, -Raj On Wednesday, March 05, 2014 11:25:26 AM, Raj Ayyampalayam wrote: I checked the version of bx-python egg and confirmed that it is bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg. I will upload the dataset to the public server and try it over there and report. Thanks, -Raj On Wednesday, March 05, 2014 11:21:56 AM, Jeremy Goecks wrote: Would it be possible that you have an old copy of the bx-python egg? You should have bx-python 0.7.1 If you check your eggs directory and you see version 0.7.1, then there may be something wrong with bx-python. In this case, please upload your build and bam to our public server and try again; if it fails on our public server, share the datasets with me and I'll take a look. Thanks, J. -- Jeremy Goecks Assistant Professor, Computational Biology Institute George Washington University On Mar 4, 2014, at 5:14 PM, Raj Ayyampalayam ra...@uga.edu mailto:ra...@uga.edu wrote: Hello, I am trying to visualize a large genome (Large number of scaffolds) and a large (bam file) in trackster on our local galaxy instance (running release_2014.02.10). When ever I try to do the above I see the following error in the logs: File bbi_file.pyx, line 215, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5596) File bbi_file.pyx, line 222, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5210) File bbi_file.pyx, line 183, in bx.bbi.bbi_file.BBIFile.summarize (lib/bx/bbi/bbi_file.c:4475) File bbi_file.pyx, line 248, in bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size (lib/bx/bbi/bbi_file.c:5656) File bpt_file.pyx, line 76, in bx.bbi.bpt_file.BPTFile.find (lib/bx/bbi/bpt_file.c:1388) File bpt_file.pyx, line 55, in bx.bbi.bpt_file.BPTFile.r_find (lib/bx/bbi/bpt_file.c:1154) AttributeError: 'BinaryFileReader' object has no attribute 'read_bits64' Trackster works OK when I load smaller data sets. It seems that there was a fix for this in bx-python code, as per mail from Jeremy (http://dev.list.galaxyproject.org/trackster-error-for-viewing-rat-data-rn5-tp4662664p4662672.html). How do I get the fixed code into my galaxy instance? Thanks, -Raj ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] [galaxy-user] Trackster error on dbkeys
(Moved to galaxy-dev mailing list because it concerns server admin rather than Galaxy usage.) If everything worked fine with a human build but not for PF3d7, then my guess is that the len file for PF3d7 isn’t correctly formatted. Right now, the file parser is very unforgiving—no extra spaces or lines are allowed. If you check the len file and don’t spot an issue, please send to it to me and I’ll take a look. Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Apr 10, 2014, at 2:30 AM, Aarthi Mohan aarthimoha...@gmail.com wrote: Hi all, I am setting up galaxy on a server running CentOS 6.5. I found that Trackster application hits me with an error Could not load chroms for this dbkey: PF3D7, when I try add new track from Visualization. I am working with Plasmodium falciparum (PF3d7) genome, and I followed the instruction for setting visualization from https://wiki.galaxyproject.org/Visualization%20Setup; and placed the 2bit, len files in the appropriate path. I have also made sure the genome build is present in the builds.txt under tool-data/shared/ucsc. For a test, I have the human chromosomes len files and Trackster loads it without any problem. Any suggestion would greatly help me. Thanks RT Log file: --- 127.0.0.1 - - [10/Apr/2014:12:29:44 +0800] GET /visualization/trackster HTTP/1.1 200 - http://127.0.0.1:8081/; Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0 127.0.0.1 - - [10/Apr/2014:12:29:45 +0800] GET /api/genomes?chrom_info=True HTTP/1.1 200 - http://127.0.0.1:8081/visualization/trackster; Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0 127.0.0.1 - - [10/Apr/2014:12:29:51 +0800] GET /api/genomes/PF3D7?low=0num=100 HTTP/1.1 500 - http://127.0.0.1:8081/visualization/trackster; Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0 Error - type 'exceptions.IndexError': list index out of range URL: http://127.0.0.1:8081/api/genomes/PF3D7?low=0num=100 File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/data/maarthi/Galaxy/Test/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/data/maarthi/Galaxy/Test/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 78 in decorator return to_json_string( func( self, trans, *args, **kwargs ) ) File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/webapps/galaxy/api/genomes.py', line 42 in show rval = self.app.genomes.chroms( trans, dbkey=id, num=num, chrom=chrom, low=low ) File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/visualization/genomes.py', line 292 in chroms rval = genome.to_dict( num=num, chrom=chrom, low=low ) File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/visualization/genomes.py', line 153 in to_dict chroms[ fields[0] ] = int( fields[1] ) IndexError: list index out of range CGI Variables - CONTENT_LENGTH: '0' HTTP_ACCEPT: 'application/json, text/javascript, */*; q=0.01' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5' HTTP_CONNECTION: 'keep-alive' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603abc74375a63eca6a53211ad8efeb084140a6e95d9de0824b221b12b4bbc465351' HTTP_HOST: '127.0.0.1:8081' HTTP_REFERER: 'http://127.0.0.1:8081/visualization/trackster' HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0' HTTP_X_REQUESTED_WITH: 'XMLHttpRequest' PATH_INFO: '/api/genomes/PF3D7' QUERY_STRING: 'low=0num=100' REMOTE_ADDR: '127.0.0.1' REQUEST_METHOD: 'GET' SERVER_NAME: '0.0.0.0' SERVER_PORT: '8081' SERVER_PROTOCOL: 'HTTP/1.1' WSGI Variables -- application: paste.recursive.RecursiveMiddleware object at 0x6b37cd0 is_api_request: True paste.cookies: (SimpleCookie: galaxysession='c6ca0ddb55be603abc74375a63eca6a53211ad8efeb084140a6e95d9de0824b221b12b4bbc465351', 'galaxysession=c6ca0ddb55be603abc74375a63eca6a53211ad8efeb084140a6e95d9de0824b221b12b4bbc465351') paste.expected_exceptions: [class 'paste.httpexceptions.HTTPException'] paste.httpexceptions: paste.httpexceptions.HTTPExceptionHandler object at 0x748eed0 paste.httpserver.thread_pool: paste.httpserver.ThreadPool
Re: [galaxy-dev] trackster is not working on the vrelease_2014.02.10--2--29ce93a13ac7
I cloned directly from galaxy-dist: % hg clone https://bitbucket.org/galaxy/galaxy-dist/ which gives you the latest release, and it is 2014.02.10--2–29ce93a13ac7 Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 29, 2014, at 3:02 AM, Shu-Yi Su s...@embl.de wrote: Hi Jeremy, Which version you download, the most latest one or vrelease_2014.02.10--2--29ce93a13ac7? Thank you very much. Best, Shu-Yi On Mar 28, 2014, at 10:47 PM, Jeremy Goecks wrote: I just downloaded a fresh copy of galaxy-dist and everything worked fine with Trackster. This suggests that your Galaxy installation is somehow corrupted. You’ll need to rollback any changes to your repository and/or start from a fresh copy. Let us know if you need help doing this. Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 27, 2014, at 4:28 AM, Shu-Yi Su shu-yi...@embl.de wrote: Hi Jeremy, I reverted the files that I have changed, and also cleaned the cache once again. The error messages are the same: Failed to load resource: the server responded with a status of 404 (Not Found) require.js:1:1910Error: Script error for: libs/backbone/backbone-relational http://requirejs.org/docs/errors.html#scripterror http://gbcs-dev/galaxy-dev/static/scripts/utils/galaxy.utils.jsFailed to load resource: the server responded with a status of 404 (Not Found) require.js:1:1910Error: Script error for: utils/galaxy.utils http://requirejs.org/docs/errors.html#scripterror Thanks a lot….. Best, Shu-Yi On Mar 27, 2014, at 12:00 AM, Jeremy Goecks wrote: The next step then is to revert all the changes that you pulled from -central and report back the errors you’re seeing. Manually pulling selected change sets can be problematic if you don’t get all the dependencies. Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 26, 2014, at 11:04 AM, Shu-Yi Su shu-yi...@embl.de wrote: Hi Jeremy, I cleaned the catche on both safari and firefox, but it doesn't work. It still shows the same error messages. Thank you very much for the help!! Best, Shu-Yi On Mar 26, 2014, at 2:00 PM, Jeremy Goecks wrote: This sounds like a cache issue. Both of these scripts have been removed from the distribution, so they should be absent from the distribution. Can you try clearing your cache and see if that fixes the issue? Thanks, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 26, 2014, at 4:39 AM, Charles Girardot charles.girar...@embl.de wrote: Hi Jeremy, After checking, the two js scripts are absent from the release: backbone-relational.js ( static/scripts/packed/libs/backbone/ ) galaxy.utils.js ( static/scripts/packed/utils/ ) bw C On 25 Mar 2014, at 16:16, Shu-Yi Su wrote: Hi Jeremy, Thank you very much for the reply. Yes, we are running on galaxy-dist, and manually pulled to update our installation. The release version is vrelease_2014.02.10--2--29ce93a13ac7. I have tried safari and firefox. Both are not working. Here is the error massage from console: [Error] Failed to load resource: the server responded with a status of 404 (Not Found) (backbone-relational.js, line 0) [Error] Failed to load resource: the server responded with a status of 404 (Not Found) (galaxy.utils.js, line 0) [Error] Error: Script error for: libs/backbone/backbone-relational http://requirejs.org/docs/errors.html#scripterror defaultOnError (require.js, line 1) onError (require.js, line 1) onScriptError (require.js, line 1) [Error] Error: Script error for: utils/galaxy.utils http://requirejs.org/docs/errors.html#scripterror defaultOnError (require.js, line 1) onError (require.js, line 1) onScriptError (require.js, line 1);;; We are also wondering if there is anything we didn't set up probably for our universe_wsgi.ini file. Thank you. Best, Shu-Yi On Mar 25, 2014, at 4:05 PM, Jeremy Goecks wrote: Providing some additional information will help diagnose the problem: *are you running galaxy-dist? If so, have you manually pulled and applied commits from galaxy-central? If so, which ones? *which Web browser are you using? *can you please open the JavaScript console in your browser and provide any errors that you see? Thanks, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 24, 2014, at 11:38 AM, Shu-Yi Su shu-yi...@embl.de wrote: Hi all, We have recently updated our local Galaxy installation to vrelease_2014.02.10--2--29ce93a13ac7 (database version is 118). I found that the Trackster is not working. I have checked the latest commits related to Trackster bugs. So i have
Re: [galaxy-dev] trackster is not working on the vrelease_2014.02.10--2--29ce93a13ac7
I just downloaded a fresh copy of galaxy-dist and everything worked fine with Trackster. This suggests that your Galaxy installation is somehow corrupted. You’ll need to rollback any changes to your repository and/or start from a fresh copy. Let us know if you need help doing this. Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 27, 2014, at 4:28 AM, Shu-Yi Su shu-yi...@embl.de wrote: Hi Jeremy, I reverted the files that I have changed, and also cleaned the cache once again. The error messages are the same: Failed to load resource: the server responded with a status of 404 (Not Found) require.js:1:1910Error: Script error for: libs/backbone/backbone-relational http://requirejs.org/docs/errors.html#scripterror http://gbcs-dev/galaxy-dev/static/scripts/utils/galaxy.utils.jsFailed to load resource: the server responded with a status of 404 (Not Found) require.js:1:1910Error: Script error for: utils/galaxy.utils http://requirejs.org/docs/errors.html#scripterror Thanks a lot….. Best, Shu-Yi On Mar 27, 2014, at 12:00 AM, Jeremy Goecks wrote: The next step then is to revert all the changes that you pulled from -central and report back the errors you’re seeing. Manually pulling selected change sets can be problematic if you don’t get all the dependencies. Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 26, 2014, at 11:04 AM, Shu-Yi Su shu-yi...@embl.de wrote: Hi Jeremy, I cleaned the catche on both safari and firefox, but it doesn't work. It still shows the same error messages. Thank you very much for the help!! Best, Shu-Yi On Mar 26, 2014, at 2:00 PM, Jeremy Goecks wrote: This sounds like a cache issue. Both of these scripts have been removed from the distribution, so they should be absent from the distribution. Can you try clearing your cache and see if that fixes the issue? Thanks, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 26, 2014, at 4:39 AM, Charles Girardot charles.girar...@embl.de wrote: Hi Jeremy, After checking, the two js scripts are absent from the release: backbone-relational.js ( static/scripts/packed/libs/backbone/ ) galaxy.utils.js ( static/scripts/packed/utils/ ) bw C On 25 Mar 2014, at 16:16, Shu-Yi Su wrote: Hi Jeremy, Thank you very much for the reply. Yes, we are running on galaxy-dist, and manually pulled to update our installation. The release version is vrelease_2014.02.10--2--29ce93a13ac7. I have tried safari and firefox. Both are not working. Here is the error massage from console: [Error] Failed to load resource: the server responded with a status of 404 (Not Found) (backbone-relational.js, line 0) [Error] Failed to load resource: the server responded with a status of 404 (Not Found) (galaxy.utils.js, line 0) [Error] Error: Script error for: libs/backbone/backbone-relational http://requirejs.org/docs/errors.html#scripterror defaultOnError (require.js, line 1) onError (require.js, line 1) onScriptError (require.js, line 1) [Error] Error: Script error for: utils/galaxy.utils http://requirejs.org/docs/errors.html#scripterror defaultOnError (require.js, line 1) onError (require.js, line 1) onScriptError (require.js, line 1);;; We are also wondering if there is anything we didn't set up probably for our universe_wsgi.ini file. Thank you. Best, Shu-Yi On Mar 25, 2014, at 4:05 PM, Jeremy Goecks wrote: Providing some additional information will help diagnose the problem: *are you running galaxy-dist? If so, have you manually pulled and applied commits from galaxy-central? If so, which ones? *which Web browser are you using? *can you please open the JavaScript console in your browser and provide any errors that you see? Thanks, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 24, 2014, at 11:38 AM, Shu-Yi Su shu-yi...@embl.de wrote: Hi all, We have recently updated our local Galaxy installation to vrelease_2014.02.10--2--29ce93a13ac7 (database version is 118). I found that the Trackster is not working. I have checked the latest commits related to Trackster bugs. So i have updated theses files: ./static/scripts/viz/trackster.js (commits date: 2014-02-28) ./static/scripts/viz/trackster_ui.js (commits date: 2014-02-28) ./static/scripts/viz/trackster/tracks.js (commits date: 2014-03-16) ./static/scripts/utils/utils.js (commits date: 2014-03-19) ./static/scripts/utils/config.js (commits date: 2014-03-15) But, it is still not working. I have tried different format…bam, bed, sam….all are not working. I looked into all possible files I can think about that might cause the problems but still don't have any clues. I also looked into the log
Re: [galaxy-dev] trackster is not working on the vrelease_2014.02.10--2--29ce93a13ac7
This sounds like a cache issue. Both of these scripts have been removed from the distribution, so they should be absent from the distribution. Can you try clearing your cache and see if that fixes the issue? Thanks, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 26, 2014, at 4:39 AM, Charles Girardot charles.girar...@embl.de wrote: Hi Jeremy, After checking, the two js scripts are absent from the release: backbone-relational.js ( static/scripts/packed/libs/backbone/ ) galaxy.utils.js ( static/scripts/packed/utils/ ) bw C On 25 Mar 2014, at 16:16, Shu-Yi Su wrote: Hi Jeremy, Thank you very much for the reply. Yes, we are running on galaxy-dist, and manually pulled to update our installation. The release version is vrelease_2014.02.10--2--29ce93a13ac7. I have tried safari and firefox. Both are not working. Here is the error massage from console: [Error] Failed to load resource: the server responded with a status of 404 (Not Found) (backbone-relational.js, line 0) [Error] Failed to load resource: the server responded with a status of 404 (Not Found) (galaxy.utils.js, line 0) [Error] Error: Script error for: libs/backbone/backbone-relational http://requirejs.org/docs/errors.html#scripterror defaultOnError (require.js, line 1) onError (require.js, line 1) onScriptError (require.js, line 1) [Error] Error: Script error for: utils/galaxy.utils http://requirejs.org/docs/errors.html#scripterror defaultOnError (require.js, line 1) onError (require.js, line 1) onScriptError (require.js, line 1);;; We are also wondering if there is anything we didn't set up probably for our universe_wsgi.ini file. Thank you. Best, Shu-Yi On Mar 25, 2014, at 4:05 PM, Jeremy Goecks wrote: Providing some additional information will help diagnose the problem: *are you running galaxy-dist? If so, have you manually pulled and applied commits from galaxy-central? If so, which ones? *which Web browser are you using? *can you please open the JavaScript console in your browser and provide any errors that you see? Thanks, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 24, 2014, at 11:38 AM, Shu-Yi Su shu-yi...@embl.de wrote: Hi all, We have recently updated our local Galaxy installation to vrelease_2014.02.10--2--29ce93a13ac7 (database version is 118). I found that the Trackster is not working. I have checked the latest commits related to Trackster bugs. So i have updated theses files: ./static/scripts/viz/trackster.js (commits date: 2014-02-28) ./static/scripts/viz/trackster_ui.js (commits date: 2014-02-28) ./static/scripts/viz/trackster/tracks.js (commits date: 2014-03-16) ./static/scripts/utils/utils.js (commits date: 2014-03-19) ./static/scripts/utils/config.js (commits date: 2014-03-15) But, it is still not working. I have tried different format…bam, bed, sam….all are not working. I looked into all possible files I can think about that might cause the problems but still don't have any clues. I also looked into the log, and there is no error, but i noticed that there is difference from the log where the trackster was working in previous installation. The log where the trackster is not working: 1. GET /galaxy-dev/visualization/trackster?dataset_id=f04ecb1d3d259245hda_ldda=hda The log where the trackster is working (from the old installation): 1. GET /galaxy/visualization/trackster?dataset_id=5d38b380cba2f4a6hda_ldda=hda…… 2. GET /galaxy/api/datasets/5d38b380cba2f4a6?hda_ldda=hdadata_type=converted_datasets_state…. 3. GET /galaxy/api/datasets/5d38b380cba2f4a6?data_type=datachrom=chr2L….. It looks like that the trackster in new version of Galaxy does not execute the second and the third steps. Here is the screen shot when i clicked View in new visualization (there is nothing shown up---blank) Any ideas or suggestions are appreciated. Thank you very much. Best, Shu-Yi PastedGraphic-1.tiff ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail
Re: [galaxy-dev] trackster is not working on the vrelease_2014.02.10--2--29ce93a13ac7
The next step then is to revert all the changes that you pulled from -central and report back the errors you’re seeing. Manually pulling selected change sets can be problematic if you don’t get all the dependencies. Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 26, 2014, at 11:04 AM, Shu-Yi Su shu-yi...@embl.de wrote: Hi Jeremy, I cleaned the catche on both safari and firefox, but it doesn't work. It still shows the same error messages. Thank you very much for the help!! Best, Shu-Yi On Mar 26, 2014, at 2:00 PM, Jeremy Goecks wrote: This sounds like a cache issue. Both of these scripts have been removed from the distribution, so they should be absent from the distribution. Can you try clearing your cache and see if that fixes the issue? Thanks, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 26, 2014, at 4:39 AM, Charles Girardot charles.girar...@embl.de wrote: Hi Jeremy, After checking, the two js scripts are absent from the release: backbone-relational.js ( static/scripts/packed/libs/backbone/ ) galaxy.utils.js ( static/scripts/packed/utils/ ) bw C On 25 Mar 2014, at 16:16, Shu-Yi Su wrote: Hi Jeremy, Thank you very much for the reply. Yes, we are running on galaxy-dist, and manually pulled to update our installation. The release version is vrelease_2014.02.10--2--29ce93a13ac7. I have tried safari and firefox. Both are not working. Here is the error massage from console: [Error] Failed to load resource: the server responded with a status of 404 (Not Found) (backbone-relational.js, line 0) [Error] Failed to load resource: the server responded with a status of 404 (Not Found) (galaxy.utils.js, line 0) [Error] Error: Script error for: libs/backbone/backbone-relational http://requirejs.org/docs/errors.html#scripterror defaultOnError (require.js, line 1) onError (require.js, line 1) onScriptError (require.js, line 1) [Error] Error: Script error for: utils/galaxy.utils http://requirejs.org/docs/errors.html#scripterror defaultOnError (require.js, line 1) onError (require.js, line 1) onScriptError (require.js, line 1);;; We are also wondering if there is anything we didn't set up probably for our universe_wsgi.ini file. Thank you. Best, Shu-Yi On Mar 25, 2014, at 4:05 PM, Jeremy Goecks wrote: Providing some additional information will help diagnose the problem: *are you running galaxy-dist? If so, have you manually pulled and applied commits from galaxy-central? If so, which ones? *which Web browser are you using? *can you please open the JavaScript console in your browser and provide any errors that you see? Thanks, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 24, 2014, at 11:38 AM, Shu-Yi Su shu-yi...@embl.de wrote: Hi all, We have recently updated our local Galaxy installation to vrelease_2014.02.10--2--29ce93a13ac7 (database version is 118). I found that the Trackster is not working. I have checked the latest commits related to Trackster bugs. So i have updated theses files: ./static/scripts/viz/trackster.js (commits date: 2014-02-28) ./static/scripts/viz/trackster_ui.js (commits date: 2014-02-28) ./static/scripts/viz/trackster/tracks.js (commits date: 2014-03-16) ./static/scripts/utils/utils.js (commits date: 2014-03-19) ./static/scripts/utils/config.js (commits date: 2014-03-15) But, it is still not working. I have tried different format…bam, bed, sam….all are not working. I looked into all possible files I can think about that might cause the problems but still don't have any clues. I also looked into the log, and there is no error, but i noticed that there is difference from the log where the trackster was working in previous installation. The log where the trackster is not working: 1. GET /galaxy-dev/visualization/trackster?dataset_id=f04ecb1d3d259245hda_ldda=hda The log where the trackster is working (from the old installation): 1. GET /galaxy/visualization/trackster?dataset_id=5d38b380cba2f4a6hda_ldda=hda…… 2. GET /galaxy/api/datasets/5d38b380cba2f4a6?hda_ldda=hdadata_type=converted_datasets_state…. 3. GET /galaxy/api/datasets/5d38b380cba2f4a6?data_type=datachrom=chr2L….. It looks like that the trackster in new version of Galaxy does not execute the second and the third steps. Here is the screen shot when i clicked View in new visualization (there is nothing shown up---blank) Any ideas or suggestions are appreciated. Thank you very much. Best, Shu-Yi PastedGraphic-1.tiff ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface
Re: [galaxy-dev] trackster is not working on the vrelease_2014.02.10--2--29ce93a13ac7
Providing some additional information will help diagnose the problem: *are you running galaxy-dist? If so, have you manually pulled and applied commits from galaxy-central? If so, which ones? *which Web browser are you using? *can you please open the JavaScript console in your browser and provide any errors that you see? Thanks, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 24, 2014, at 11:38 AM, Shu-Yi Su shu-yi...@embl.de wrote: Hi all, We have recently updated our local Galaxy installation to vrelease_2014.02.10--2--29ce93a13ac7 (database version is 118). I found that the Trackster is not working. I have checked the latest commits related to Trackster bugs. So i have updated theses files: ./static/scripts/viz/trackster.js (commits date: 2014-02-28) ./static/scripts/viz/trackster_ui.js (commits date: 2014-02-28) ./static/scripts/viz/trackster/tracks.js (commits date: 2014-03-16) ./static/scripts/utils/utils.js (commits date: 2014-03-19) ./static/scripts/utils/config.js (commits date: 2014-03-15) But, it is still not working. I have tried different format…bam, bed, sam….all are not working. I looked into all possible files I can think about that might cause the problems but still don't have any clues. I also looked into the log, and there is no error, but i noticed that there is difference from the log where the trackster was working in previous installation. The log where the trackster is not working: 1. GET /galaxy-dev/visualization/trackster?dataset_id=f04ecb1d3d259245hda_ldda=hda The log where the trackster is working (from the old installation): 1. GET /galaxy/visualization/trackster?dataset_id=5d38b380cba2f4a6hda_ldda=hda…… 2. GET /galaxy/api/datasets/5d38b380cba2f4a6?hda_ldda=hdadata_type=converted_datasets_state…. 3. GET /galaxy/api/datasets/5d38b380cba2f4a6?data_type=datachrom=chr2L….. It looks like that the trackster in new version of Galaxy does not execute the second and the third steps. Here is the screen shot when i clicked View in new visualization (there is nothing shown up---blank) Any ideas or suggestions are appreciated. Thank you very much. Best, Shu-Yi PastedGraphic-1.tiff ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] read_bits64 error when loading large genomes/data into trackster
Would it be possible that you have an old copy of the bx-python egg? You should have bx-python 0.7.1 If you check your eggs directory and you see version 0.7.1, then there may be something wrong with bx-python. In this case, please upload your build and bam to our public server and try again; if it fails on our public server, share the datasets with me and I'll take a look. Thanks, J. -- Jeremy Goecks Assistant Professor, Computational Biology Institute George Washington University On Mar 4, 2014, at 5:14 PM, Raj Ayyampalayam ra...@uga.edu wrote: Hello, I am trying to visualize a large genome (Large number of scaffolds) and a large (bam file) in trackster on our local galaxy instance (running release_2014.02.10). When ever I try to do the above I see the following error in the logs: File bbi_file.pyx, line 215, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5596) File bbi_file.pyx, line 222, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5210) File bbi_file.pyx, line 183, in bx.bbi.bbi_file.BBIFile.summarize (lib/bx/bbi/bbi_file.c:4475) File bbi_file.pyx, line 248, in bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size (lib/bx/bbi/bbi_file.c:5656) File bpt_file.pyx, line 76, in bx.bbi.bpt_file.BPTFile.find (lib/bx/bbi/bpt_file.c:1388) File bpt_file.pyx, line 55, in bx.bbi.bpt_file.BPTFile.r_find (lib/bx/bbi/bpt_file.c:1154) AttributeError: 'BinaryFileReader' object has no attribute 'read_bits64' Trackster works OK when I load smaller data sets. It seems that there was a fix for this in bx-python code, as per mail from Jeremy (http://dev.list.galaxyproject.org/trackster-error-for-viewing-rat-data-rn5-tp4662664p4662672.html). How do I get the fixed code into my galaxy instance? Thanks, -Raj ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] HTML form of select parameter
On Jan 27, 2014, at 9:57 AM, John Chilton chil...@msi.umn.edu wrote:
The swap over happens when
the number of items gets sufficiently large and a jQuery-based widget
called select2 replaces all select boxes in Galaxy - unless explicitly
disabled. I understand the desire to disable this. I am not sure
anyone is really very pleased with select2 for multiple select widgets
- it might be worth just disabling it for multiple select form
elements all together globally. I don't know.
The function 'replace_big_select_inputs' in galaxy.base.js is where the logic
for this code is located. You could avoid applying select2 to selects with
multiple using the following CSS selector on line 261 in place of $('select'):
$('select').not('[multiple]')
Best,
J.___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] faToTwoBit: not found / trackster
Ok, then it's very likely a PATH issue. There's no magic needed here -
faToTwoBit simply needs to be on your path. It seems you've tried debugging
this already; one suggestion is to provide the full path to the executable and
see if that works.
--
Jeremy Goecks
Assistant Professor, Computational Biology Institute
George Washington University
On Jan 6, 2014, at 1:49 AM, Jasper Jan Koehorst jasper.koeho...@wur.nl wrote:
To give a better answer, when I enter the command this is what I get:
:~$ faToTwoBit
faToTwoBit - Convert DNA from fasta to 2bit format
usage:
faToTwoBit in.fa [in2.fa in3.fa ...] out.2bit
options:
-noMaskIgnore lower-case masking in fa file.
-stripVersion Strip off version number after '.' for GenBank accessions.
-ignoreDupsConvert first sequence only if there are duplicate sequence
names. Use 'twoBitDup' to find duplicate sequences.
2014/1/4 Jasper Koehorst jasperkoeho...@gmail.com
Yes and i even chmodded it to 777 for testing purposes. When I run it
I get the option overview of the tool. I can't copy that right now
(out of office) but the application works as I also 2bitted a genome.
On 04 Jan 2014, at 18:37, Jeremy Goecks jeremy.goe...@emory.edu wrote:
Can you run the faToTwoBit tool from the command line? It can be difficult
to find the right executable for UCSC tools sometimes; if you have the
wrong executable (e.g. 32 bit instead of 64 bit), you'll see the misleading
'not found' error.
Best,
J.
On Jan 3, 2014, at 11:35 AM, Jasper Jan Koehorst
jasper.koeho...@wur.nlmailto:jasper.koeho...@wur.nl wrote:
First of all, best wishes!
I was/am trying to visualize a GTF file in galaxy on a local 64 bit ubuntu
system. However I stumbled upon an issue were it remained grey. When I did
an automaic visualization I saw a line that went up and down over the
chromosome. When I switched to pack I got a grey / / / line slashed output.
I contacted dannon and ceberhard on IRC and they told me to add a print
statement on line 200 for the tracker. This visualized the following error:
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
So I downloaded and placed the faToTwoBit file in /usr/bin I even chmodded
it to 777 but the error remained. I also started digging into the code on
where it calls the application and added /usr/bin/ in front of it but no
luck so far.
Anyone has a clue on what is happening? It almost must be an ubuntu related
issue as I dont see how galaxy cannot find the path.
$PATH is still properly set when running galaxy as I added echo $path it to
a tool and it returned
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/bin
The IRC chat can be seen here:
http://pastebin.com/9fZrkRDn
Thanks a lot,
/home/galaxy/HB27.2bit10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=0high=320487mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/31.0.1650.63 Safari/537.36
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=1602432high=1894876mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/31.0.1650.63 Safari/537.36
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=1281945high=1602432mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/31.0.1650.63 Safari/537.36
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=320486high=640973mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/31.0.1650.63 Safari/537.36
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=961459high=1281946mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0
Re: [galaxy-dev] faToTwoBit: not found / trackster
Ok, then it's very likely a PATH issue. There's no magic needed here -
faToTwoBit simply needs to be on your path. It seems you've tried debugging
this already; one suggestion is to provide the full path to the executable and
see if that works.
--
Jeremy Goecks
Assistant Professor, Computational Biology Institute
George Washington University
On Jan 6, 2014, at 1:49 AM, Jasper Jan Koehorst jasper.koeho...@wur.nl wrote:
To give a better answer, when I enter the command this is what I get:
:~$ faToTwoBit
faToTwoBit - Convert DNA from fasta to 2bit format
usage:
faToTwoBit in.fa [in2.fa in3.fa ...] out.2bit
options:
-noMaskIgnore lower-case masking in fa file.
-stripVersion Strip off version number after '.' for GenBank accessions.
-ignoreDupsConvert first sequence only if there are duplicate sequence
names. Use 'twoBitDup' to find duplicate sequences.
2014/1/4 Jasper Koehorst jasperkoeho...@gmail.com
Yes and i even chmodded it to 777 for testing purposes. When I run it
I get the option overview of the tool. I can't copy that right now
(out of office) but the application works as I also 2bitted a genome.
On 04 Jan 2014, at 18:37, Jeremy Goecks jeremy.goe...@emory.edu wrote:
Can you run the faToTwoBit tool from the command line? It can be difficult
to find the right executable for UCSC tools sometimes; if you have the
wrong executable (e.g. 32 bit instead of 64 bit), you'll see the misleading
'not found' error.
Best,
J.
On Jan 3, 2014, at 11:35 AM, Jasper Jan Koehorst
jasper.koeho...@wur.nlmailto:jasper.koeho...@wur.nl wrote:
First of all, best wishes!
I was/am trying to visualize a GTF file in galaxy on a local 64 bit ubuntu
system. However I stumbled upon an issue were it remained grey. When I did
an automaic visualization I saw a line that went up and down over the
chromosome. When I switched to pack I got a grey / / / line slashed output.
I contacted dannon and ceberhard on IRC and they told me to add a print
statement on line 200 for the tracker. This visualized the following error:
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
So I downloaded and placed the faToTwoBit file in /usr/bin I even chmodded
it to 777 but the error remained. I also started digging into the code on
where it calls the application and added /usr/bin/ in front of it but no
luck so far.
Anyone has a clue on what is happening? It almost must be an ubuntu related
issue as I dont see how galaxy cannot find the path.
$PATH is still properly set when running galaxy as I added echo $path it to
a tool and it returned
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/bin
The IRC chat can be seen here:
http://pastebin.com/9fZrkRDn
Thanks a lot,
/home/galaxy/HB27.2bit10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=0high=320487mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/31.0.1650.63 Safari/537.36
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=1602432high=1894876mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/31.0.1650.63 Safari/537.36
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=1281945high=1602432mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/31.0.1650.63 Safari/537.36
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=320486high=640973mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/31.0.1650.63 Safari/537.36
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=961459high=1281946mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla
Re: [galaxy-dev] faToTwoBit: not found / trackster
Can you run the faToTwoBit tool from the command line? It can be difficult to
find the right executable for UCSC tools sometimes; if you have the wrong
executable (e.g. 32 bit instead of 64 bit), you'll see the misleading 'not
found' error.
Best,
J.
On Jan 3, 2014, at 11:35 AM, Jasper Jan Koehorst jasper.koeho...@wur.nl wrote:
First of all, best wishes!
I was/am trying to visualize a GTF file in galaxy on a local 64 bit ubuntu
system. However I stumbled upon an issue were it remained grey. When I did an
automaic visualization I saw a line that went up and down over the
chromosome. When I switched to pack I got a grey / / / line slashed output.
I contacted dannon and ceberhard on IRC and they told me to add a print
statement on line 200 for the tracker. This visualized the following error:
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
So I downloaded and placed the faToTwoBit file in /usr/bin I even chmodded it
to 777 but the error remained. I also started digging into the code on where
it calls the application and added /usr/bin/ in front of it but no luck so
far.
Anyone has a clue on what is happening? It almost must be an ubuntu related
issue as I dont see how galaxy cannot find the path.
$PATH is still properly set when running galaxy as I added echo $path it to a
tool and it returned
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/bin
The IRC chat can be seen here:
http://pastebin.com/9fZrkRDn
Thanks a lot,
/home/galaxy/HB27.2bit10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=0high=320487mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/31.0.1650.63 Safari/537.36
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=1602432high=1894876mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/31.0.1650.63 Safari/537.36
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=1281945high=1602432mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/31.0.1650.63 Safari/537.36
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=320486high=640973mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/31.0.1650.63 Safari/537.36
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=961459high=1281946mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/31.0.1650.63 Safari/537.36
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=640972high=961459mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/31.0.1650.63 Safari/537.36
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:36,418 Error in
dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py,
line 46, in show
rval = self._data( trans, dataset, **kwd )
File /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py,
line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=320486high=640973mode=Packresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 500 -
Re: [galaxy-dev] faToTwoBit: not found / trackster
Can you run the faToTwoBit tool from the command line? It can be difficult to
find the right executable for UCSC tools sometimes; if you have the wrong
executable (e.g. 32 bit instead of 64 bit), you'll see the misleading 'not
found' error.
--
Jeremy Goecks
Assistant Professor, Computational Biology Institute
George Washington University
On Jan 3, 2014, at 11:35 AM, Jasper Jan Koehorst jasper.koeho...@wur.nl wrote:
First of all, best wishes!
I was/am trying to visualize a GTF file in galaxy on a local 64 bit ubuntu
system. However I stumbled upon an issue were it remained grey. When I did an
automaic visualization I saw a line that went up and down over the
chromosome. When I switched to pack I got a grey / / / line slashed output.
I contacted dannon and ceberhard on IRC and they told me to add a print
statement on line 200 for the tracker. This visualized the following error:
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
So I downloaded and placed the faToTwoBit file in /usr/bin I even chmodded it
to 777 but the error remained. I also started digging into the code on where
it calls the application and added /usr/bin/ in front of it but no luck so
far.
Anyone has a clue on what is happening? It almost must be an ubuntu related
issue as I dont see how galaxy cannot find the path.
$PATH is still properly set when running galaxy as I added echo $path it to a
tool and it returned
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/bin
The IRC chat can be seen here:
http://pastebin.com/9fZrkRDn
Thanks a lot,
/home/galaxy/HB27.2bit10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=0high=320487mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/31.0.1650.63 Safari/537.36
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=1602432high=1894876mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/31.0.1650.63 Safari/537.36
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=1281945high=1602432mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/31.0.1650.63 Safari/537.36
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=320486high=640973mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/31.0.1650.63 Safari/537.36
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=961459high=1281946mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/31.0.1650.63 Safari/537.36
10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=640972high=961459mode=Autoresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP/1.1 200 -
http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbfhda_ldda=hda;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/31.0.1650.63 Safari/537.36
{'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:36,418 Error in
dataset API at listing contents: 'data': 'data'
Traceback (most recent call last):
File /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py,
line 46, in show
rval = self._data( trans, dataset, **kwd )
File /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py,
line 201, in _data
ref_seq = data_dict[ 'data' ]
KeyError: 'data'
10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] GET
/api/datasets/e2132aef71b11dbf?data_type=datachrom=chrlow=320486high=640973mode=Packresolution=801.216067653277hda_ldda=hdafilter_cols=%5B%22Score%22%5D
HTTP
Re: [galaxy-dev] trackster error for viewing rat data (rn5)
When visualizing a BAM dataset, Galaxy generates a bigwig dataset of read coverage. Trying to visualize this dataset is causing the issue. You could try to convert the BAM to BigWig manually (click on dataset's pencil icon -- convert format -- convert to bigwig) and see if there are any issues generating the dataset. You could then try visualizing that dataset directly to see if anything unusual happens. Finally, there was a bug in bx-python that was fixed a while back: https://bitbucket.org/james_taylor/bx-python/commits/24893a84ce13a18815e3006c9f89b3828022ac96 if you're using an old version of Galaxy, you might try updating and see if that fixes the issue. Best, J. On Nov 22, 2013, at 8:18 AM, Shu-Yi Su shu-yi...@embl.de wrote: Hi Jeremy, Thank you so much for reply. You are right…..I just took the first few lines in fastq file and mapped with bowtie. Now it works with this small dataset. I am trying to find the error in my complete dataset, but haven't spotted any yet. Do you think the error is from reading the read name or position or something else…..this could help me to dig out the error in the file? Thank you again for the help….without this piece of useful information, i might had spent days and days on this : ) Best regards, Shu-Yi On Nov 22, 2013, at 2:40 AM, Jeremy Goecks wrote: This appears to be an issue with the dataset that you're trying to view, not the build or visualization. It appears that the (bigwig? bigbed?) dataset is malformed in some way. Can you inspect the dataset to look for errors? Are you able to view a different rn5 dataset? J. On Nov 21, 2013, at 10:43 AM, Shu-Yi Su shu-yi...@embl.de wrote: Hi, I am trying to view rat data (rn5) using trackster with data format bam or bigwig on our galaxy installation, but it isn't working. It works with other organisms, such as dm3 or hg19. There is error message in the log: 10.11.70.120 - - [20/Nov/2013:16:14:21 +0200] GET /galaxy-dev/api/genomes/rn5?low=0num=100 HTTP/1.1 200 - http://gbcs-dev/galaxy-dev/visualization/trackster?dataset_id=83c20bbc7104922bhda_ldda=hda; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.30.1 (KHTML, like Gecko) Version/6.0.5 Safari/536.30.1 10.11.70.120 - - [20/Nov/2013:16:14:21 +0200] GET /galaxy-dev/api/datasets/83c20bbc7104922b?hda_ldda=hdadata_type=track_config HTTP/1.1 200 - http://gbcs-dev/galaxy-dev/visualization/trackster?dataset_id=83c20bbc7104922bhda_ldda=hda; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.30.1 (KHTML, like Gecko) Version/6.0.5 Safari/536.30.1 galaxy.webapps.galaxy.api.datasets ERROR 2013-11-20 16:14:21,795 Error in dataset API at listing contents: 'BinaryFileReader' object has no attribute 'read_bits64': 'BinaryFileReader' object has no attribute 'read_bits64' Traceback (most recent call last): File /g/funcgen/galaxy-dev/lib/galaxy/webapps/galaxy/api/datasets.py, line 44, in show is_true( kwd.get( 'retry', False ) ) ) File /g/funcgen/galaxy-dev/lib/galaxy/webapps/galaxy/api/datasets.py, line 106, in _converted_datasets_state if not data_provider.has_data( chrom ): File /g/funcgen/galaxy-dev/lib/galaxy/visualization/data_providers/genome.py, line 1078, in has_data all_dat = bbi.query( chrom, 0, 2147483647, 1 ) or \ File bbi_file.pyx, line 215, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5596) File bbi_file.pyx, line 222, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5210) File bbi_file.pyx, line 183, in bx.bbi.bbi_file.BBIFile.summarize (lib/bx/bbi/bbi_file.c:4475) File bbi_file.pyx, line 248, in bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size (lib/bx/bbi/bbi_file.c:5656) File bpt_file.pyx, line 76, in bx.bbi.bpt_file.BPTFile.find (lib/bx/bbi/bpt_file.c:1388) File bpt_file.pyx, line 55, in bx.bbi.bpt_file.BPTFile.r_find (lib/bx/bbi/bpt_file.c:1154) AttributeError: 'BinaryFileReader' object has no attribute 'read_bits64' I also attached the first few lines in our rn5.len: chr1290094216 chr2285068071 chr4248343840 chr3183740530 chr5177180328 chr6156897508 chrX154597545 chr7143501887 chr8132457389 chr9121549591 chr13 118718031 chr14 115151701 chr15 114627140 chr10 112200500 chr11 93518069 chr17 92503511 chr16 90051983 chr18 87229863 chr19 72914587 chr20 57791882 chr12 54450796 chr4_AABR06109730_random227955 chrUn_JH620568 73090 chr2_JH620298_random62026 chr5_JH620330_random58807 chrUn_JH620520 57992 chrUn_JH620553 56877 chr1_AABR06109393_random52834 chr18_JH620420_random 51685 chr9_JH620364_random51490 chrX_JH620445_random49212 chrUn_JH620623 47760 chr10_JH620371_random 44089 I have looked into this error for a while and still can't figure it out. Any
Re: [galaxy-dev] reasonable linux box specs
Without details about your incoming data rate and size, it's very difficult to answer this question. I suggest taking some of your data, running it on our public server (usegalaxy.org), and seeing how long it takes. RNA-seq tools (Tophat, Cufflinks, etc.) use 4 cores for a job, so you can estimate how many cores you might need (as well as estimate disk space). I was mistaken: RNA-seq tools use 8 cores on our public server. Best, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] reasonable linux box specs
Without details about your incoming data rate and size, it's very difficult to answer this question. I suggest taking some of your data, running it on our public server (usegalaxy.org), and seeing how long it takes. RNA-seq tools (Tophat, Cufflinks, etc.) use 4 cores for a job, so you can estimate how many cores you might need (as well as estimate disk space). You might also look at using Galaxy on the cloud as well: http://wiki.galaxyproject.org/CloudMan Good luck, J. On Nov 14, 2013, at 7:07 PM, Andrew Norman anorma...@gmail.com wrote: Hi all I'd like to set up a local installation of Galaxy on a dedicated linux machine. I've taken a look at the Galaxy appliance, but since I'm the only one in my lab who will be using it, it's outside my price range. I'm going to be doing RNA seq read mapping and differential expression analysis. Can anyone recommend some minimum specs for the machine? I understand that more memory/cores will enable faster processing, but I'm willing to wait overnight for results to save some cash. Any advice you have about this will be helpful! Thanks, Andy ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Empty tool panel
Do you see any errors in the JavaScript console? Does this only happen on particular Web browsers? J. On Nov 15, 2013, at 10:15 AM, Yec'han Laizet ylai...@pierroton.inra.fr wrote: Hi, In the current version of galaxy stable branch (5c789ab4144a), the tool panel is empty when installed (freshly and out of the box) on my production server (ubuntu server 12.04). If I copy this galaxy folder onto my laptop, the tool panel shows up (ubuntu 13.10). Do you have an idea of what could be the problem? Thanks Yec'han Dr. Yec'han LAIZET Ingenieur Bioinformatique Tel: +33 (0)5 57 12 27 75 _ Plateforme Genome Transcriptome INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Why are Custom Builds disabled when
Why are Custom Builds only enabled if you're *not* using remote_user ? Is this because they're related to user preferences (as per the code in lib/galaxy/webapps/galaxy/controllers/user.py)? This may be an artifact of a time when user preferences were immutable. Do Custom Builds and Preferences work on your set up using remote users? And then a followup, if I have to add a build using either a FASTA file or a lenfile and editing the Galaxy install on the server, where do I need to make changes? Unfortunately, It'll go in different places depending on your use. What are you looking to do with the build? Thanks, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Share workflows for all users
For your workflow, try going to 'Share or Publish' option -- and share via URL (and publish it if you want). The workflow can then be shared with a large number of people using the URL. Best, J. On Oct 21, 2013, at 4:07 AM, Anatoliy Pandorin pandorin...@gmail.com wrote: For a long time I used release_2013.01.13. And to share workflows for all users galaxy used a simple link to workflow (exp: url/workflow/run?id=cbbbf59e8f08c98c ) This was done by my simple script. (copied links to welcome page) Moving on release_2013.08.12 this method does not work anymore. You first need add users to Share Workflow with Individual Users. It is without a doubt correct. But: As now distribute(Share) workflow for all users at once? Maybe I do not understand that. Pardon Best regards, Anatoly ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] page editor problem when saving Chinese
This issue was fixed in this changeset:
https://bitbucket.org/galaxy/galaxy-central/commits/8c663e656f64a60dac55979841947e78ce23a473
If you update your Galaxy to the revision on galaxy-dist this problem should go
away.
Best,
J.
On Oct 18, 2013, at 1:10 PM, lardo la...@qq.com wrote:
I run a local instance of galaxy and edit content of a page, error occurs
when the content contains Chinese:
URL: http://127.0.0.1:8080/page/save
Module weberror.evalexception.middleware:364 in respond
app_iter = self.application(environ, detect_start_response)
Module paste.recursive:84 in __call__
return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
body = method( trans, **kwargs )
Module galaxy.web.framework:98 in decorator
return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.page:566 in save
trans.sa_session.flush()
Module sqlalchemy.orm.scoping:114 in do
Module sqlalchemy.orm.session:1718 in flush
Module sqlalchemy.orm.session:1789 in _flush
Module sqlalchemy.orm.unitofwork:331 in execute
Module sqlalchemy.orm.unitofwork:475 in execute
Module sqlalchemy.orm.persistence:64 in save_obj
Module sqlalchemy.orm.persistence:558 in _emit_insert_statements
Module sqlalchemy.engine.base:1449 in execute
Module sqlalchemy.engine.base:1584 in _execute_clauseelement
Module sqlalchemy.engine.base:1698 in _execute_context
Module sqlalchemy.engine.base:1691 in _execute_context
Module sqlalchemy.engine.default:331 in do_execute
ProgrammingError: (ProgrammingError) You must not use 8-bit bytestrings
unless you use a text_factory that can interpret 8-bit bytestrings (like
text_factory = str). It is highly recommended that you instead just switch
your application to Unicode strings. u'INSERT INTO page_revision
(create_time, update_time, page_id, title, content) VALUES (?, ?, ?, ?, ?)'
('2013-10-18 17:09:01.226991', '2013-10-18 17:09:01.227000', 1, u'test',
'paavdx/pp\xe4\xb8\xad/p')
[]
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Re: [galaxy-dev] Access to history_id from tool config XML
I'm still not fully understanding your usage scenario. A simple example is the creation of a full history based log file. I imagine that this would be an ideal use of the history API. Rather than having tools log history, write a script that uses the API to generate a history log. My more detailed need is to parallel an existing analysis pipeline in galaxy, using the same underlying code. Reusing the same code from within galaxy has the great advantage of ensuring exactly the same process is run, allowing the official analysis to be repeated by outsiders. This pipeline works on a number of inputs (paired end reads, multiple replicates, etc.) and goes through a number of intervening steps where massive temporary files may be reused in several steps, then ultimately deleted after obtaining final results. The existing pipeline, outside of galaxy, creates these shared files in a temporary directory, exclusive to the experiment being run. In Galaxy however, ensuring that an experiment named by one user will not collide with one named by another user, accidentally overwriting existing files becomes a great deal easier if the temporary experiment directories have history_id based names. Why not use mktemp() to ensure a unique directory that can house an experiment's data? Since the histories could be shared among multiple users, the user_id will not be effective. How are Galaxy histories shared amongst users? J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff version
The problem is likely a collision on the tool_id; update the tool ID for one of the wrappers and that should solve the problem. Best, J. On Sep 24, 2013, at 5:30 PM, Curtis Hendrickson (Campus) wrote: Jeremy, We didn’t have time to factor out to toolshed just now, so we took the following approach 1. Take 1.3-compatible cuffdiff wrapper (0.0.5) and move it to cuffdiff_1.3_wrapper.py/xml – and add a dependency on cufflinks verson=1.3.0 (and set that up). 2. Apply your patch, changing current cuffdiff wrapper to (0.0.6) 3. Add a line in tool_conf.xml so that both your modern cuffdiff v6 wrapper and our cuffdiff v5 wrappers are included. When we restarted, and went to the GUI, there was only ONE cuffdiff tool listed, and when you clicked on it, it brought up the 0.0.5 version (the 2nd listed in tool_conf). There was no version pull down to get the 0.0.6 version., Any idea what I’ve missed? Regards, Curtis From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Thursday, September 19, 2013 3:17 PM To: Curtis Hendrickson (Campus) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff version We can hack the old wrapper back in, using a hard-coded path to the old cuffdiff. You could also use Managed Tool Dependencies for multiple versions of cuffdiff: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies Shantanu suggests it might be a better world if we create a tool-shed repository for the cuffdiff 1.3-2.1 (wrapper 0.0.5) version, then install that. Would that be a better path, or just add confusion? This is on the right path. The right thing to do is migrate the Cuff* tool wrappers out of the galaxy-central/dist repositories; this is a bit more effort than simply creating the tool-shed repository for the wrappers. There are two reasons I haven't done this: (a) time; (b) because the tools—and consequently the wrappers—are still in active development, there needs to be a place for managing development of the wrappers. Hence, the wrappers need a home on bitbucket or github, but we (the Galaxy team) haven't determined where these wrappers should live. (a) is a much more significant barrier than (b), so if a pull request migrating Cuff* tools out of the distribution were made, I'm sure (b) could be worked out. Best, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff version
Jeremy, I’m sure that would get both tools to show up, but it seems to me that would miss the goal of past/future reproducibility. My goal is to have to two versions of the program available at the same time – Cuffdiff_wrapper 0.0.5 (cuffdiff/links 1.3) the historical one that all the current histories/workflows reference, so those don’t break, and Cuffdiff_wrapper 0.0.6 (cuffdiff/links 2.1) the new version for use going forward, which has a distinct version so that those histories/workflows are reproducible and the choice of which version to use is the users. I want to avoid someone who wants to re-run last-month’s cuffdiff with slightly different parameters being forced (w/o their knowledge) to run a more recent version of cuffdiff – which would then give an apples to oranges comparison. With 2 versions of the same ID installed, I expected to either see two listings in the tool pane AND/OR a version pulldown on the cuffdiff tool params pane. Is the only way to get two versions of the same tool id installed via toolshed? Yes. Unfortunately, it's not possible to manually install multiple versions of the same tool; the development efforts of the Galaxy team are focused on multiple version installation via only the tool shed for now. However, we'd welcome a pull request that adds this functionality to Galaxy. Given that you want to provide backward compatibility, it's probably best to keep the tool_id for the older Cuffdiff wrapper and change the new one; mercurial merges should handle this change gracefully as it's small. Best, J. Sorry – I feel like I’ve mis-understood the tool version/id resolution architecture. Happy to talk on the phone if that would be a better use of your time. Thanks, Curtis From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Wednesday, September 25, 2013 8:43 AM To: Curtis Hendrickson (Campus) Cc: galaxy-dev@lists.bx.psu.edu; Shantanu Pavgi (Campus) Subject: Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff version The problem is likely a collision on the tool_id; update the tool ID for one of the wrappers and that should solve the problem. Best, J. On Sep 24, 2013, at 5:30 PM, Curtis Hendrickson (Campus) wrote: Jeremy, We didn’t have time to factor out to toolshed just now, so we took the following approach 1. Take 1.3-compatible cuffdiff wrapper (0.0.5) and move it to cuffdiff_1.3_wrapper.py/xml – and add a dependency on cufflinks verson=1.3.0 (and set that up). 2. Apply your patch, changing current cuffdiff wrapper to (0.0.6) 3. Add a line in tool_conf.xml so that both your modern cuffdiff v6 wrapper and our cuffdiff v5 wrappers are included. When we restarted, and went to the GUI, there was only ONE cuffdiff tool listed, and when you clicked on it, it brought up the 0.0.5 version (the 2nd listed in tool_conf). There was no version pull down to get the 0.0.6 version., Any idea what I’ve missed? Regards, Curtis From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Thursday, September 19, 2013 3:17 PM To: Curtis Hendrickson (Campus) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff version We can hack the old wrapper back in, using a hard-coded path to the old cuffdiff. You could also use Managed Tool Dependencies for multiple versions of cuffdiff: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies Shantanu suggests it might be a better world if we create a tool-shed repository for the cuffdiff 1.3-2.1 (wrapper 0.0.5) version, then install that. Would that be a better path, or just add confusion? This is on the right path. The right thing to do is migrate the Cuff* tool wrappers out of the galaxy-central/dist repositories; this is a bit more effort than simply creating the tool-shed repository for the wrappers. There are two reasons I haven't done this: (a) time; (b) because the tools—and consequently the wrappers—are still in active development, there needs to be a place for managing development of the wrappers. Hence, the wrappers need a home on bitbucket or github, but we (the Galaxy team) haven't determined where these wrappers should live. (a) is a much more significant barrier than (b), so if a pull request migrating Cuff* tools out of the distribution were made, I'm sure (b) could be worked out. Best, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Visualisation of VCF files in trackster
Thanks for reporting this issue and workaround Ulf. I've committed a fix that addresses this issue by only includeing the -split option for BED/GFF/GTF datasets and not VCF: https://bitbucket.org/galaxy/galaxy-central/commits/b8d8f81bed872e58b4691643de8a08fa41662e71 Best, J. On Sep 12, 2013, at 6:45 AM, Ulf Schaefer wrote: Dear Jeremy Thank you for your reply and sorry for not being clear. In short I solved the problem. Below is some info, in case this is useful for someone else. Thanks for your help The situation was: On Main: Visualisation of the SAM/BAM file - OK Visualisation of the VCF file - OK On my local install: Visualisation of the SAM/BAM file - OK Visualisation of the VCF file - FAIL The reason is that this command fails: grep -v '^#' /data/database/files/000/dataset_596.dat | sort -k1,1 | bedtools genomecov -bg -split -i stdin -g /data/database/files/000/dataset_598.dat temp.bg ; bedGraphToBigWig temp.bg /data/database/files/000/dataset_598.dat /data/database/files/000/dataset_609.dat with Input error: found interval with block-counts not matching starts/sizes Where dataset_596.dat is my vcf and /data/database/files/000/dataset_598.dat is my genome file. This is produced by the bedtools genomecov bit of the command, which appears to have some sort of problem with the vcf input in combination with the -split option. The problem disappears with the installation of the latest version of bedtools (v2.17.0), but if you are using the version that you get from yum (v2.15.0) you run into this error. Ulf ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ** ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Access to history_id from tool config XML
At line ~694: incoming['__user_name__'] = user_name + if job.history and job.history.id: + incoming['__history_id__'] = job.history.id + else: + incoming['__history_id__'] = 'unknown' I have tested this change and it appears to give me exactly what I want. My question: does this change appear correct Yes, the change is correct. and can it be incorporated into the main galaxy code-base? Can you provide a usage scenario for including history_id in the tool dict? Thanks, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff version
I know the general versioning problem is address through the tool-shed mechanism, but for the remaining core wrappers, can maintainersplease update wrapper version numbers when making changes? Not bumping wrapper versions is an oversight, not deliberate. For this wrapper set, how would you advise us to support both? Fortunately, I refactored the Cuffdiff wrapper recently and correctly bumped the tool version: https://bitbucket.org/galaxy/galaxy-central/commits/6a32d26aefc758cf576e0b753c2626ac56005c18 You can either pull this changeset manually or wait until the next distribution in early October to get the changeset. Best, J.___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff version
We can hack the old wrapper back in, using a hard-coded path to the old cuffdiff. You could also use Managed Tool Dependencies for multiple versions of cuffdiff: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies Shantanu suggests it might be a better world if we create a tool-shed repository for the cuffdiff 1.3-2.1 (wrapper 0.0.5) version, then install that. Would that be a better path, or just add confusion? This is on the right path. The right thing to do is migrate the Cuff* tool wrappers out of the galaxy-central/dist repositories; this is a bit more effort than simply creating the tool-shed repository for the wrappers. There are two reasons I haven't done this: (a) time; (b) because the tools—and consequently the wrappers—are still in active development, there needs to be a place for managing development of the wrappers. Hence, the wrappers need a home on bitbucket or github, but we (the Galaxy team) haven't determined where these wrappers should live. (a) is a much more significant barrier than (b), so if a pull request migrating Cuff* tools out of the distribution were made, I'm sure (b) could be worked out. Best, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] CuffDiff read group tracking
You can overwrite your copy of the Cuffdiff wrapper at tools/ngs_rna/cuffdiff_wrapper.xml with the new version: https://bitbucket.org/galaxy/galaxy-central/raw/48fad71361b3075c85c7d365dd52c106cabad73a/tools/ngs_rna/cuffdiff_wrapper.xml Best, J. On Sep 16, 2013, at 5:36 PM, Matthew Paul wrote: Hey Galaxy, I am trying to use CuffDIff with replicate analysis on a local instance. I saw that Jeremy Goecks had a solution to this problem: http://user.list.galaxyproject.org/Cuffdiff-changes-tt4655893.html#a4655901. Could I see/use this source code please? I can't really wait until the next update. Thanks, Matt Paul ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Geek question re HTTP POST and Galaxy
hi Jeremy, in the histories controller, I could find no example to nicely obtain the PUT and POST content payload. Am I missing it? So I think a bad answer to my question is the following code. But I really don't like my _get_payload() hack reaching into the trans.environ object. Is there a better way to do this? The short answer is that Galaxy has middleware that unpacks API request content and puts them into parameters. For example, the URL /api/histories/2f3f601bb97a6a89 calls histories/index with id=2f3f601bb97a6a89 The data from a POST or PUT appears as payload for create/update methods. in buildapp.py // I also don't like the fact that it needs five separate calls. this is the sort of design pattern that should be very easy. webapp.mapper.connect(/api/assets/, controller=medbook, action=assets_create, conditions=dict(method=[POST])) webapp.mapper.connect(/api/assets/, controller=medbook, action=assets_read, conditions=dict(method=[GET])) webapp.mapper.connect(/api/assets/*url, controller=medbook, action=assets_read, conditions=dict(method=[GET])) webapp.mapper.connect(/api/assets/*url, controller=medbook, action=assets_update, conditions=dict(method=[PUT])) webapp.mapper.connect(/api/assets/*url, controller=medbook, action=assets_delete, conditions=dict(method=[DELETE])) Something like this should work for all five: webapp.mapper.resource( 'asset', 'assets', path_prefix='/api' ) In general, your best bet is to replicate an existing API controller as closely as you can. J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Conditional and validator: refresh_on_change without validation
You're not missing anything; using validators is the right way for checking parameter values. However, the page refreshes + validation errors is certainly less than ideal for usability. We're in the process of transitioning tool forms to a JavaScript-based framework so that full page refreshes (and associated validation checks) are no longer necessary. J. On Sep 11, 2013, at 4:26 AM, Kahlke Tim wrote: Hi I'm using the validator tag for simple sanity checks of a tool input. But I realized that any conditional in the form will automatically call refresh_on_change which also validates all fields and prints errror messages. So questioin: is there a more galaxy-like way of checking input parameters? I am aware of the possibility to do sanity checks through custom code (http://wiki.galaxyproject.org/Admin/Tools/Custom%20Code) but the page states it should only be done if there is no other way. Regards, Tim ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Geek question re HTTP POST and Galaxy
Take a look at the histories controller (histories.py) for an example + documentation on how Galaxy realizes a RESTful interface. In short, you'll want to implement different methods for create, read, update, and delete. Kwds are miscellaneous parameters included in a request that are not explicitly specified in a method signature. Good luck, J. On Sep 13, 2013, at 7:52 PM, Ted Goldstein, Ph.D. wrote: I've been knocking my head over this all afternoon and I was hoping to buy a vowel, use a lifeline, whatever. I'm trying to use the Ember JS framework (which is very nice) for some extensions. It relies heavily on a REST model using the same method with all of the HTTP forms including ActionHTTP Verb URL Find GET /people/123 Find All GET /people UpdatePUT /people/123 (with the HTTP payload packed with the JSON content) CreatePOST/people DeleteDELETE /people/123 How can I make an API function that responds to all five forms and what should be in buildapp.py? All of the code in Galaxy currently uses the kwd (keyword) parameter. But there are no keywords here. Confused, Ted ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Scaling and hardware requirements
This isn't an easy question to answer. Here's why: *there is significant variation in mammalian genome size; of course, larger genomes require more resources, but the relationship is difficult to quantify; *assembly can take anywhere from a day to a week depending on software and resource choices; *variant detection can take anywhere from 1-4 days depending on software used; *completing assembly and variant detection in 48 hours is something that is challenging for even the most advanced genomics labs. To answer your question, I'd start with 256-512GB of RAM on a machine and 36-72 compute cores across a cluster. This is simply a guess of course. Before investing in hardware, you might try your analysis on the cloud ( usegalaxy.org/cloud ) to get a sense of the resources needed. Good luck, J. On Sep 11, 2013, at 8:34 AM, Gerald Bothe wrote: Can I put in a similar question on top of this: How much resources do you need for re-sequencing of a mammalian genome (assembly and variant detection), one job at a time? E.g. how much RAM etc. if I want the re-sequencing SAM file of a 30-fold coverage be done in 48 hours? Gerald Gerald Bothe 32 Plum Hill Road East Lyme, CT 06333 (860) 451 8776 From: Nikos Sidiropoulos nikos.sid...@gmail.com To: Peter Cock p.j.a.c...@googlemail.com Cc: galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu Sent: Wednesday, September 11, 2013 8:19 AM Subject: Re: [galaxy-dev] Scaling and hardware requirements Hi Peter It's going to be one big machine, running both Galaxy server and the jobs. It's going to be a multi-process configuration. If that idea is terribly bad please let me know so I can give back the feedback. De novo assembly can also be for the human/mouse genome. Bests, Nikos 2013/9/11 Peter Cock p.j.a.c...@googlemail.com On Wed, Sep 11, 2013 at 1:03 PM, Nikos Sidiropoulos nikos.sid...@gmail.com wrote: Hi all, I have a couple of questions regarding a server setup dedicated on Galaxy. The idea is to buy a 64 core 256GB RAM server. From my experience I believe that Galaxy will be able to scale up to 64 cpu's but I would like some more feedback on this. Also, is 4GB RAM per CPU core enough for NGS data? (including de-novo assembly) Bests, Nikos Hi Nikos, Is this going to be one server both for running Galaxy (which needs fairly low resources) and running jobs for Galaxy, like de novo assemblies (which need high resources)? i.e. You have one big machine only, no cluster? For de novo assembly the RAM per core/CPU isn't important, it is the total RAM on the machine. How much RAM you need depends on which assembler you use, the organism (both size and also complexity) and the volume of data. What you've described should be fine for bacterial assemblies and smaller eukaryotes - beyond that you'll need to give more details. Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Visualisation of VCF files in trackster
My attempts to visualise a vcf file in trackster fail. I can visualise the corresponding SAM/BAM files fine. I can visualise the same file on Galaxy main too, but not in my local install. To be clear, you can visualize the VCF dataaset on main but not locally? Can you visualize SAM/BAM datasets locally? One guess is that you may need to install and add tabix and bgzip to your path. J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Deseq2 wrapper question
STAR aligner I have a partial STAR wrapper that may be useful: https://bitbucket.org/jgoecks/jeremys-code/src/d7096c132657420f08b540c6954b947f648aac80/galaxy/tool-wrappers/star.xml?at=default Whether you use this code or not, I do have one request: please put the output in BAM rather than SAM format in order to save disk space. Best, J.___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Circumvent Show all button
There is currently no simple way to circumvent this behavior. If you want to modify the code, take a look at display_data() in data.py -- you'll want to bump up the max_peek_size (line 351 in -central) above 10 MB for HTML datasets. Good luck, J. On Sep 9, 2013, at 6:16 AM, Gromobir wrote: Hey guys, Just one short question: Is there any way to circumvent the Show all dialog within galaxy, if the data I would like to display is too large? I would like to display some xhtml files, which can really have a lot of lines and I don't want the users of my tool to click on this button every time before accessing the page. Any hints are highly appreciated. Best regards, Gromobir ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] options from_dataset evaluation in workflow
Dear all, in one of my tools I'm populating a list of possible choices from a file in the history using the options from_dataset tag. Now using the tool as part of a workflow, the choices are not calculated at the setup stage, but I have to enter free-text and Galaxy seems to evaluate whether that's a legal choice only when the specific tool starts running (way down in my workflow). Is there any workaround for this behavior, so that choices are presented before workflow execution? In general, no, the dataset content is not known at workflow runtime so the options field cannot be populated then. However, in the special case that the options_from_dataset tag is used for a tool that has a direct input dataset for the workflow, this would be possible (and desirable); for this case, a Trello card would be useful. Best, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] API question: is it possible to start exporting histories
Is it currently possible to export histories via the API? Not possible yet but is definitely something we'd like to implement and/or see from a community contribution. Best, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Trackster: alignment is not showing up as 'squish'
I suspect there is an issue with Trackster when changing from one mode to another. Can you confirm that by saving and refreshing the visualization, you can view the dataset in different modes? Thanks, J. On Sep 5, 2013, at 4:06 AM, Joachim Jacob | VIB | wrote: Update: the 'dense' option does not work neither. So in summary: the alignment can only be viewed in 'coverage' mode. Thanks, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 09/05/2013 09:52 AM, Joachim Jacob | VIB | wrote: Hi all, I have a problem that the mappings of an experiment suddenly don't show up anymore in Trackster, only when I choose 'squish' as visualisation format. 'Coverage' and 'dense' provide the expected output. So 'squish' shows nothing. But 'Pack' shows only the names, without the bars. Note: 'squish' and 'pack' used to work. Currently I am on 2013_08_12. Other mappings (from other experiments) show up as expected. The 2 cases side by side in this screenshot (thanks to the scratchbook functionality!): https://dl.dropboxusercontent.com/u/18352887/Selection_151.png Thanks for any help, Joachim ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] [galaxy-user] Questions regarding Galaxy Tool XML File
Question: How save is the optional attribute ? I mean how consequent are you in this matter when the tool definition xml is to be created. It's not clear to me what you're asking. That said, it's important to distinguish between Galaxy tool wrappers and their corresponding tools. Either deliberately or inadvertently, the wrapper may have different behavior than the tool. For example, an optional tool parameter may not be optional in the Galaxy wrapper because the wrapper author believes that explicitly setting a value is critical. Is there any relation to the conditional tag ? No relation, but there can certainly be some confusion between conditional and optional parameters. It's not clear what the best way to solve this issue is. Another question: Have you ever thought about pipes. It seems that the tool xml schema entirely ignores it. For instance one could easily tag an input parameter to be able to read from stdin or to write to stdout/stderr. Especially samtools and bedtools do support pipes. Is there an obvious reason not to use it ? Galaxy's treats each tool run autonomously right now; e.g., each tool run is submitted to the cluster as a separate job. This approach prevents pipes from being used. However, we are definitely interested in extending Galaxy to support piping in the future. J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] How to configure and set up the Circos on my local Galaxy?
Please take a look at this page for setting up visualizations: http://wiki.galaxyproject.org/Visualization%20Setup Let us know if you have any questions. Best, J. On Sep 1, 2013, at 9:37 PM, shenwiyn wrote: Hi , I found that the visualization of Circos works greatly in Galaxy main,but failed on my local Galaxy.I want to find out some information about configuring and setting up the Circos on local Galaxy,I saw nothing inhttp://wiki.galaxyproject.org/New%20Visualization%20Page#Circos_plot_.28aka_Circster.29 .Please any suggestions would be most welcome. shenwiyn ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Select multiple and conditional
As you discovered, this isn't possible yet. You'll need to break up your
parameters into multiple conditions, so Yes/No for Blast and Yes/No for Fasta.
Best,
J.
On Aug 26, 2013, at 6:33 AM, Kahlke Tim wrote:
Hei,
Is it possible to use a select multiple=True for a conditional? I'm
trying to use it for checkboxes which by default have to have multiple set.
But as soon as I put the multiple-tag in I get an 'no case matched' exception
(see example below).
Any suggestions?
Tim
Example (working)
conditional name=c1
param type=select name=dbt label=Db tools
option value=blastBlast/option
option value=fastaFasta/option
/param
when value=blast
...
/when
/conditional
Example (exception)
conditional name=c1
param type=select name=dbt label=Db tools multiple=True
option value=blastBlast/option
option value=fastaFasta/option
/param
when value=blast
...
/when
/conditional
= Exception: ('No class matched value:' , 'c1' , None)
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Re: [galaxy-dev] RuntimeError: maximum recursion depth exceeded while calling a Python object
There are sporadic reports of this issue, but I haven't been able to reproduce it. My best guess is that it's due to trying to use the custom build before Galaxy has finished creating it. To ensure that the custom build is ready for use, make sure to wait for Galaxy to show the number of chromosomes rather than '?' on the custom builds page. It also sometimes happens when I create and share a Trackster visualization. I can access the visualization without problem whereas the users I shared it with can't access it because of the mentioned error or they get a message like Can't load dbkey. Can't load dbkey is a different issue than the server error. If you can provide datasets and/or steps to reproduce either issue, I'm confident that they could be fixed. Thanks, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Why does my trackster complain about not being able to display BED files?
It appears you are missing some updates. This issue was fixed in this changeset
9992:
--
changeset: 9992:7105c53139d4
branch: stable
parent: 9990:f35c0441e374
user:jeremy goecks jeremy.goe...@emory.edu
date:Tue Jun 11 17:34:26 2013 -0400
files: lib/galaxy/tools/actions/__init__.py
description:
Use len_file_path config option rather than hardcoded path for chromInfo tool
parameter.
--
You might have missed this changeset if you updated to the late June release
soon after it came out. However, it is definitely included in the August
release. Can you confirm that you're running the August release?
Thanks,
J.
On Aug 23, 2013, at 9:08 PM, Thon de Boer wrote:
Ofcourse I spoke too soon…
I get a problem in that the conversion of my dataset reports that it cannot
find the chromosome length files, even though trickster itself has no problem
showing it…
I looked at the problem script and it is showing below
It seems that the script is passed the path to the chromosome files like this
“tool-data/shared/ucsc/chrom/hg19-decoy.len”
This will clearly never work since this file is not relative to the working
directory..
SO somewhere a script forgets to add the ${GALAXY_DATA_DIR} or whatever that
parameter is…..
I could probably hardcode the location of the tool-data directory, but I
don’t think that should be the solution…
Why do I only have this issue? SHOULD I have hardcoded the location of
tool-data?
The universe_wgi.ini.sample file does not hardcode this…
Am I missing some updates?
Thanks,
Thon
#!/bin/sh
GALAXY_LIB=None
if [ $GALAXY_LIB != None ]; then
if [ -n $PYTHONPATH ]; then
PYTHONPATH=$GALAXY_LIB:$PYTHONPATH
else
PYTHONPATH=$GALAXY_LIB
fi
export PYTHONPATH
fi
TMPDIR=/mnt/ngs/analysis/svcgalaxy/DATATEST/TMP
export TMPDIR
cd /mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916
grep -v '^#' /mnt/ngs/analysis/svcgalaxy/DATATEST/files/002/dataset_2288.dat
| sort -k1,1 | bedtools genomecov -bg -split -i stdin
-gtool-data/shared/ucsc/chrom/hg19-decoy.len temp.bg ;
bedGraphToBigWig temp.bg
tool-data/shared/ucsc/chrom/hg19-decoy.len/mnt/ngs/analysis/svcgalaxy/DATATEST/files/002/dataset_2315.dat;
cd /mnt/ngs/analysis/svcgalaxy/galaxy-test;
/mnt/ngs/analysis/svcgalaxy/galaxy-test/set_metadata.sh
/mnt/ngs/analysis/svcgalaxy/DATATEST/files
/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916 .
/mnt/ngs/analysis/svcgalaxy/galaxy-test/universe_wsgi.ini
/mnt/ngs/analysis/svcgalaxy/DATA/TMP/tmp2KAn7W
/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/galaxy.json
/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/metadata_in_HistoryDatasetAssociation_2551_XsCZer,/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/metadata_kwds_HistoryDatasetAssociation_2551_iNUAr_,/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/metadata_out_HistoryDatasetAssociation_2551_ZHhosg,/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/metadata_results_HistoryDatasetAssociation_2551_tqtiIX,,/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/metadata_override_HistoryDatasetAssociation_2551_MOfd8w
echo $?
/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/galaxy_1916.ec
Regards,
Thon
Thon deBoer Ph.D., Bioinformatics Guru
California, USA |p: +1 (650) 799-6839 |m: thondeb...@me.com
Public profile on LinkedIn
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Thon de Boer
Sent: Friday, August 23, 2013 5:47 PM
To: 'Jeremy Goecks'
Cc: 'Galaxy-dev Galaxy-dev'
Subject: Re: [galaxy-dev] Why does my trackster complain about not being able
to display BED files?
I tracked it down to a problem with the API proxy configuration.
I had the API calls diverted to a different server since I wanted to ensure
that API calls would be handled by a different server, but that does not seem
to work correctly for the API calls used in trickster…
Issue resolved…
Regards,
Thon
Thon deBoer Ph.D., Bioinformatics Guru
California, USA |p: +1 (650) 799-6839 |m: thondeb...@me.com
Public profile on LinkedIn
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Thon de Boer
Sent: Friday, August 23, 2013 5:12 PM
To: 'Jeremy Goecks'
Cc: 'Galaxy-dev Galaxy-dev'
Subject: Re: [galaxy-dev] Why does my trackster complain about not being able
to display BED files?
I now have a different problem with a different (production) version of
galaxy trickster.
I always get this message “Could not load chroms for this dbkey”
I have checked that I have files with the [key].len in
tool-data/shared/ucsc/chrom and I have twobit files etc.
The weird thing is, that the “Create
Re: [galaxy-dev] enable to edit pages
This bug has been fixed in our code repository and will be included in our next
release, which is due out in a couple weeks.
Best,
J.
On Aug 1, 2013, at 1:25 AM, Philipe Moncuquet wrote:
Hi guys,
Since the last update of Galaxy. We are enable to edit pages on our local
instance. Pages can be viewed without problems but not editing. The server
error we get is as foolow, any advice would be greatly appreciated.
URL:
http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa331b3e
Module galaxy.web.framework.middleware.error:149 in __call__
app_iter = self.application(environ, sr_checker)
Module paste.recursive:84 in __call__
return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
body = method( trans, **kwargs )
Module galaxy.web.framework:98 in decorator
return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.page:446 in edit_content
return trans.fill_template( page/editor.mako, page=page )
Module galaxy.web.framework:957 in fill_template
return self.fill_template_mako( filename, **kwargs )
Module galaxy.web.framework:969 in fill_template_mako
return template.render( **data )
Module mako.template:296 in render
return runtime._render(self, self.callable_, args, data)
Module mako.runtime:660 in _render
**_kwargs_for_callable(callable_, data))
Module mako.runtime:692 in _render_context
_exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
Module mako.runtime:718 in _exec_template
callable_(context, *args, **kwargs)
Module _base_base_panels_mako:125 in render_body
__M_writer(unicode(self.center_panel()))
Module page_editor_mako:196 in render_center_panel
__M_writer(unicode(page.latest_revision.content.decode('utf-8')))
Module encodings.utf_8:16 in decode
return codecs.utf_8_decode(input, errors, True)
UnicodeEncodeError: 'ascii' codec can't encode character u'\u2019' in
position 1709: ordinal not in range(128)
Regards,
Philippe
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Re: [galaxy-dev] How to display tool instead of html WWFSMD page at start-up?
Yes, this works on my local instance. Did you restart your Galaxy instance after adding the welcome_url setting? On Jul 29, 2013, at 11:02 PM, neil.burd...@csiro.au wrote: Yes I tried that but I still only see the default welcome.html page. Have you got this to work? Thanks Neil From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Tuesday, 30 July 2013 12:37 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: ross.laza...@gmail.com; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] How to display tool instead of html WWFSMD page at start-up? You'll need to add the setting further down in the config file, such as under the 'UI Localization' section. Best, J. On Jul 29, 2013, at 8:49 PM, neil.burd...@csiro.au wrote: Thanks Jeremy, But this doesn’t seem to work. If I add the welcome_url to the universe_wsgi.ini (is this the universe config file you mentioned?) as shown below, I continue to get the welcome.html page # Galaxy --- # Configuration of the Galaxy application. [app:main] filter-with = proxy-prefix cookie_path = /csiro welcome_url = /tool_runner?tool_id=upload1 If I move the welcome_url higher up in the universe_wsgi.ini file I get an error the last part is shown below: File /home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py, line 190, in invoke return filter(filtered) File /home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py, line 130, in filter_wrapper **context.local_conf) File /home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/util/fixtypeerror.py, line 57, in fix_call val = callable(*args, **kw) TypeError: make_prefix_middleware() got an unexpected keyword argument 'welcome_url' I can’t find anywhere in the code that has the test string “welcome_html” Any ideas? Thanks Neil From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Tuesday, 30 July 2013 7:32 AM To: Ross Cc: Burdett, Neil (ICT Centre, Herston - RBWH); galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] How to display tool instead of html WWFSMD page at start-up? There's an undocumented setting in the universe config, welcome_url, that can be used; if you point this as follows it will bring up the upload tool. welcome_url = /tool_runner?tool_id=upload1 On Jul 29, 2013, at 3:28 AM, Ross wrote: Neil, good news: the initial center panel renders static/welcome.html so easy to change. bad news: AFAIK no way to show a (dynamic) default tool form instead - others may know more.. On Mon, Jul 29, 2013 at 5:03 PM, neil.burd...@csiro.au wrote: Hi, When Galaxy is started the centre column displays the “Hello world! It’s running ...” WWFSMD? Html Page. How can this be changed so that a tool i.e. get data tool is shown up on start-up with all its text boxes etc rather than the default html file? Is this possible? Thanks Neil ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] How to display tool instead of html WWFSMD page at start-up?
You'll need to add the setting further down in the config file, such as under the 'UI Localization' section. Best, J. On Jul 29, 2013, at 8:49 PM, neil.burd...@csiro.au wrote: Thanks Jeremy, But this doesn’t seem to work. If I add the welcome_url to the universe_wsgi.ini (is this the universe config file you mentioned?) as shown below, I continue to get the welcome.html page # Galaxy --- # Configuration of the Galaxy application. [app:main] filter-with = proxy-prefix cookie_path = /csiro welcome_url = /tool_runner?tool_id=upload1 If I move the welcome_url higher up in the universe_wsgi.ini file I get an error the last part is shown below: File /home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py, line 190, in invoke return filter(filtered) File /home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py, line 130, in filter_wrapper **context.local_conf) File /home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/util/fixtypeerror.py, line 57, in fix_call val = callable(*args, **kw) TypeError: make_prefix_middleware() got an unexpected keyword argument 'welcome_url' I can’t find anywhere in the code that has the test string “welcome_html” Any ideas? Thanks Neil From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Tuesday, 30 July 2013 7:32 AM To: Ross Cc: Burdett, Neil (ICT Centre, Herston - RBWH); galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] How to display tool instead of html WWFSMD page at start-up? There's an undocumented setting in the universe config, welcome_url, that can be used; if you point this as follows it will bring up the upload tool. welcome_url = /tool_runner?tool_id=upload1 On Jul 29, 2013, at 3:28 AM, Ross wrote: Neil, good news: the initial center panel renders static/welcome.html so easy to change. bad news: AFAIK no way to show a (dynamic) default tool form instead - others may know more.. On Mon, Jul 29, 2013 at 5:03 PM, neil.burd...@csiro.au wrote: Hi, When Galaxy is started the centre column displays the “Hello world! It’s running ...” WWFSMD? Html Page. How can this be changed so that a tool i.e. get data tool is shown up on start-up with all its text boxes etc rather than the default html file? Is this possible? Thanks Neil ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] HTML output with external Javascript
The file that Gift is producing is already an html file and there's already an html datatype in Galaxy by default. The output file in question just invokes remote javascript libraries inside script tags, and this seems to be tripping up Galaxy's data viewer. Setting up relative paths to images and scripts inside your HTML output should work; this is done in FastQC and other similar tools. We've tried downloading and referencing the javascript libraries in /static/js as well. This should work as well and is the approach used by the rGenetics tools, but the path you want is /static/scripts/ Note that Galaxy already has many jQuery libraries in /static/scripts/libs/jquery, which could simplify development. I know that the new visualization platform in Galaxy uses a lot of external javascript libraries like D3Š does anyone know how that is being handled differently? For now, the viz framework is a different code base that's not relevant for displaying datasets. Best, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tool input is folder rather than file
You'll want to use composite datatypes: http://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes On Jul 24, 2013, at 3:08 AM, Pankaj Narang wrote: Dear Developers, I want to design a tool whose input is folder containing files and sub-folders. I was wandering which value should I assign to TYPE attribute of PARAM tag in INPUTS. -- Best regards, Pankaj Narang ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] FastQC files are not being recognized by
Fastq datasets can have many different encodings for quality scores. See here for details: http://en.wikipedia.org/wiki/FASTQ_format Many tools in Galaxy require that fastq datasets be in fastqsanger format and designated as such in its datatype. Because your data appears to be in Sanger/Illumina 1.9 format, you can simply change the datatype (click on the pencil icon to change the datatype). If you have fastq datasets in other encodings, you can use the FastQ groomer tool to convert it to Sanger format. Best, J. On Jul 18, 2013, at 9:41 PM, Ricardo Perez wrote: Dear all, We are doing some processes in our server that use fastq files. We have obtained the data in .sra format and then convert them into fastq format using the sra tool kit. However, when we upload this files into galaxy, some tools does not recognize the file as fastq. When we apply FasQC:Read QC, under summary statistics it says that encoding is Sanger / Illumina 1.9. Is this an error of our part while installing galaxy in our server? Thank you for your time, --Ricardo Perez ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tool inheritance
What you envision probably isn't possible yet. Two ideas for extending Galaxy: (1) use the show structure functionality from the history menu to generate a summary page or (2) create a Pages API and implement a function to create and save a new page that describes the structure. Best, J. On Jul 17, 2013, at 4:15 PM, Lee Katz wrote: One more question for the Galaxy gurus. I have a series of tools that 1) interleave raw reads, 2) assemble them, and 3) predict genes from the assembly. How can I display inheritance on the data produced from these tools? It would be really nice if a set of genes showed that they came from an assembly, which came from a set of raw reads. I can't find this on the site, and so I am sure I am using the wrong keywords or something... Thank you! -- Lee Katz, Ph.D. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] cummerBund installation
The toolshed has a wrapper for cummerbund: http://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund On Jul 12, 2013, at 12:03 AM, sridhar srinivasan wrote: Dear Developers, Could you please tell me the possibilities of using the R package cummeRband for visualization of RNA-seq data in galaxy?? Thanks Sridhar ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Trackster and bedtools error
bedtools genomecov -bg -split -i stdin -g /usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len However this crashes. After looking in my computer, I find that bedtools do not contain the file genomecov. Is this an erroneous assumption of mine or have I installed something wrong? genomecov is not a file, it is a parameter that indicates what operation to run. My guess is that you may have an old version of BEDtools installed; in this case, you'll need to update BEDtools. At minimum, BEDtools versions 2.15+ will work fine with Trackster/Galaxy. You can type this into your terminal to see the BEDtools version: bedtools --version Good luck, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Exit_code not working anymore
This is a known issue that we have plans to fix. You can follow our progress here: https://trello.com/c/JfB2w1Br Best, J. On Jul 12, 2013, at 6:09 AM, Mathieu Bahin wrote: Hi all, We have a Galaxy instance that we are regularly keeping up to date following the Galaxy main, so we have the current version (fd4113962c32 commit). For us, since a few updates (unfortunately, I don't know when it started), the exit_code tag is not working anymore. I made the simplest tool to confirm : tool id=tool_to_come name=tool_to_come description/description command interpreter=bash test.sh $input $output /command inputs param name=input type=text value=7 label=Param / /inputs outputs data name=output format=fasta label=Output / /outputs stdio exit_code range=12 level=fatal description=Grave probleme ! / /stdio help **Tool documentation** /help /tool --- #!/bin/bash set -e if [ $1 -ne 10 ]; then exit 12 else echo Yeah ! $2 fi Anyway, it still doesn't work as it used to... Am I the only one to have the problem ? Can you help me ? Cheers, Mathieu (Rennes - France) ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Short-term access to a galaxy server for teaching
Here's a cloud image that the Galaxy team often uses for workshops: http://wiki.galaxyproject.org/CloudWorkshop Good luck, J. On Jul 11, 2013, at 1:28 PM, Maddhi, Srinivas wrote: Hi Max, An alternative approach, in case that becomes necessary, would be to set up your own temporary instance of Galaxy in the Amazon Web Services (AWS) Cloud as described at http://wiki.galaxyproject.org/CloudMan. Another Cloud-based option: if interested in installing Galaxy on an auto-scaling HPC cluster in the AWS Cloud from the command line, I can provide the instructions to do so. The instructions were designed to allow those with access to a browser on a Linux, Mac or Windows [1] system and minimal computing experience perform the installation. Time to get Galaxy up and running using this method is estimated at one to two hours. Good luck! Notes: 1. Will require installation of Putty or similar program for secure access to the AWS virtual machine, 2. Both options mentioned above could be overkill, although eminently feasible, if all you need is Galaxy running on a single server, 3. Additional options are listed at http://wiki.galaxyproject.org/Big%20Picture/Choices -- Srinivas Maddhi Senior Systems Administrator Iowa Institute for Human Genetics ITS Research Services, The University of Iowa -Original Message- From: Max Heiman hei...@genetics.med.harvard.edu Date: Thursday, July 11, 2013 9:16 AM To: galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu Subject: [galaxy-dev] Short-term access to a galaxy server for teaching Hi, We would like to use Galaxy to introduce genomic analysis in our introductory graduate genetics course. Would anyone be willing to let us borrow a server for two hours (9-11 am Boston time, Sept 25)? The students will be uploading ~1M 30-bp reads, running QC and trimming barcodes, using BOWTIE to align them to the yeast genome and then MACS to call peaks. There will be about 40 users total. Each task runs quickly on the public server, but we are concerned about the queue times when dealing with a 90-min class. Thank you for any help or advice, best Max ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] queue system
You have two options: (1) set the number of workers in the LocalJobRunner; (2) Galaxy can use many different computing clusters, all of which have queuing systems that you can control. See this page for more details on both options: http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Local Good luck, J. On Jul 10, 2013, at 7:18 AM, Jasper Jan Koehorst wrote: Is it possible to create a queue system for separate jobs. I have a module which roughly consumes all CPUs on our machine and if another user decides to run the same module with other data it should wait till all other runs are finished to prevent overloading. Is there a setting for this? Jasper Koehorst Wageningen UR ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Trackster and bedtools error
You'll need to make sure that bedtools is in your Galaxy user's path. Best, J. On Jul 9, 2013, at 6:40 PM, Perez, Ricardo wrote: Dear all, As I was trying to do visualize my data set in trackster, I get the following error: /bin/sh: 1: bedtools: not found sort: fflush failed: standard output: Broken pipe sort: write error needLargeMem: trying to allocate 0 bytes (limit: 1000) When doing a sudo find / -name bedtools in my system, I get the following output: /usr/share/bedtools /usr/share/doc/bedtools Do I have bedtools installed in the wrong place? Thank you for your help, --Ricardo Perez ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Question about bowtie2_indeces.loc
Dbkey specifies the base assembly; unique build ID species the particular assembly. This is most often used for human assemblies: dbkey is hg19 and build ID might specify some combinations of autosomes, sex chromosomes, and mitichondrial DNA. J. On Jul 6, 2013, at 6:16 PM, Perez, Ricardo wrote: Dear all, When adding a genome I understand that the format are added in the following way: unique_build_id dbkey display_name file_base_path My question is, what is the difference between the unique_build_id and the dbkey? Thank you for your time, --Ricardo Perez ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] samtools BAM to SAM tmp directory
In the spirit of this solution, I've implemented something similar in -central changeset: https://bitbucket.org/galaxy/galaxy-central/commits/c7a07f350887fe3b4e822ba6b26b63ac3ac14bdf The tool now creates temporary files in its working directory, which can be configured via the 'job_working_directory' setting; you might choose to set this to the same value as 'new_file_path' for simplicity. Best, J. On Jul 1, 2013, at 8:32 AM, Nicolas Delhomme wrote: Hej Matt! This has been bugging me as well since we are running galaxy locally with a server that has a very restricted space for the /tmp directory. Here are the change I made to the sam-to-bam tools to have him writing to new_file_path rather than $TMP. First in the xml file (1.1.2 is the original version of the file in the June 2013 release) delhomme:samtools$ diff sam_to_bam.xml sam_to_bam.xml_1.1.2 1c1 tool id=sam_to_bam name=SAM-to-BAM version=1.1.3 --- tool id=sam_to_bam name=SAM-to-BAM version=1.1.2 8d7 --temp=$__app__.config.new_file_path And in the python file: delhomme:samtools$ diff sam_to_bam.py sam_to_bam.py_1.1.2 5d4 --temp: hidden option to set the tmp directory 39d37 parser.add_option( '', '--temp', dest='temp', help='The temporary directory to use for writing tmp files' ) 61d58 os.remove( tmp ) 63d59 os.remove( tmp ) 74c70 tmp_dir = tempfile.mkdtemp( dir=options.temp ) --- tmp_dir = tempfile.mkdtemp() For the galaxy developers - I don't know if there's a way in the galaxy API to do this more easily. If there's I'd love to hear about it. If not it would be a great addition. Cheers, Nico --- Nicolas Delhomme Nathaniel Street Lab Department of Plant Physiology Umeå Plant Science Center Tel: +46 90 786 7989 Email: nicolas.delho...@plantphys.umu.se SLU - Umeå universitet Umeå S-901 87 Sweden --- On Apr 9, 2012, at 10:53 PM, Matt Shirley wrote: Is there a reason that the samtools BAM to SAM does not respect the new_file_path set in the config file? The tmp directory handling by different tool wrappers seems to be an issue right now on systems with small system tmp directories. -- Matt Shirley Ph.D Candidate - BCMB Pevsner Lab Johns Hopkins Medicine ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Insert link in page editor
Can anyone comment on this? Why insert a weird non-user friendly WYM stamp guid? Just unfinished functionality. It's fixed in -central changeset 2cabbf368763 and will be available on our public server in a couple weeks. Best, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Upload files to data library
To follow up on that, I thought it would be useful to have that mentioned in the wiki. I did some modifications to indicate the necessary changes to be done to universe_wgi.ini file (http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles). I hope that is OK. Besides, the screenshots are a bit outdated, since the option selection mode seemingly has changed. I'll try to change the screenshots as well. This is fantastic and much appreciated Lionel! We definitely encourage additions/updates to the wiki by the community. Best, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Upload files to data library
You'll need to update the settings in your universe_wgi.ini file (and restart Galaxy) to get these options to show up; specifically, take a look at 'library_import_dir' and 'allow_library_path_paste' Best, J. On Jun 28, 2013, at 2:22 AM, Lionel Guy wrote: Hi! I'm trying to upload multiple files a data library on my local instance of Galaxy. I've looked at the tutorial on the Galaxy wiki (http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles), where it's said that there are four options to upload files, available by clicking the arrow at the top of the page one gets to when clicking on the add dataset button. However, although the tutorial shows the text Create new data library datasets with an arrow next to it, the page I get to when clicking on Add datasets shows Upload files to a data library with no arrow. I thus cannot add files otherwise than by uploading files one by one. Did I miss something? Am I doing anything wrong? I'm using: $ hg tip changeset: 10003:b4a373d86c51 tag: tip parent: 10001:471484ff8be6 Thanks for your help! Lionel Uppsala University ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Bowtie2 Specifying -k value (Alignment Search)
I was looking at galaxy/dist/tools/sr_mapping/bowtie2_wrapper.* and it does not seem to challenging to add another field where a user could specify some integer value that we simply pass to the the command tag in the xml file. Would this be the correct way to go about this? Yes, this is correct; the -X or -I option are good examples of using integer parameters. The Bowtie2 wrapper has never been fleshed out; if you do decided to add options, please consider submitting a pull request so that others can benefit from your work as well. Best, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Path to the bedtools for getting trackster working properly
To have Trackster visualization working properly in Galaxy, one needs bedtools. Yet in our instance (running under Ubuntu OS), installing bedtools in the galaxy home directory and setting the environmental variable PATH in the .profile file so that it includes the path to ~/bin/bedtools does not work. Yet the PATH variable is indeed including the appropriate information as the owner of the galaxy home directory can run the bedtools in command lines. I have also to precise that we use a lot of third party tools (bowtie, cufflinks, etc...) including wigToBigWig which is also required for trackster, and that we have no path problem with these tools. Indeed the only way to get galaxy accessing properly to the bedtools currently is to put the bedtools in the /usr/local/bin directory. Here it works ! I suspect it is a problem of shell specification when the bedtools are used for trackster, but I could not figure out further the issue. It's difficult to speculate about what's going on. Trackster uses the same infrastructure (PATH, submission script, etc.) for running bedtools that other Galaxy tools use, so there's reason to think that Trackster requires something special in any way. I also have multiple instances where bedtools is installed alongside bowtie/cufflinks/tophat/wigToBigWig/etc. in a single bin directory that is in the Galaxy user's path, and that works for me. You could certainly modify the conversion tools that Trackster uses to echo and inspect the PATH. Let us know if you find anything interesting. Best, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] validation for tools
dwgsim (and dwgsimeval) may be useful to you: http://toolshed.g2.bx.psu.edu/view/nilshomer/dwgsim http://toolshed.g2.bx.psu.edu/view/nilshomer/dwgsim_eval Good luck, J. On Jun 24, 2013, at 11:47 PM, מירב . wrote: Hi, I want to do some checks on tools I'm using(in this case I'm checking svdetect). I have a program that creats .fasta file of genome with some structural variants. Now I need a tool wich will simulate the illumina's sequencing read and output .fastq files(or .sam files). Does galaxy have such tool? If not, do you have suggestion for something out of galaxy? Thanks for your help merav ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error in using Trackster: datatypes_conf.xml
A converted for this file is not installed. Please heck your datatypes_conf.xml file. How exactly do I find out which converted files I am missing? This information isn't easy to find yet, so I've created a card for it: https://trello.com/c/E3ReiSVU If you haven't modified your datatypes_conf.xml, you can copy datatypes_conf.xml.sample to datatypes_conf.xml and the converter error should go away. FYI, the complete instructions for setting up visualizations in Galaxy can be found here: http://wiki.galaxyproject.org/Visualization%20Setup Let us know if you run into other issues. Best, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] API updating meta data for a history
Take a look at the item_tags API controller; you can manage (add/delete/show) history, dataset, and workflow tags using it. There's not much documentation for it yet, but it should be pretty straight-forward. Let us know if you have questions. Best, J. On Jun 20, 2013, at 9:59 AM, Philip Mabon wrote: Hey, I was curious if it was possible to allow the API to change tags associated with a history? At the moment in the galaxy code it's forbidden. Having the ability to add tags using the API would be helpful of associating multiple histories to a particular project. So later, it would be easier to 'select' all the histories to perform a bulk action. Ie download all contigs.fasta from histories that tag with 'project_Ecoli_June20_2013'. Thanks Phil ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] simplest way to connect RNAseq tools for a local Galaxy instance
Here's some specific information about what the PATH variable is for UNIX systems and how to set it: http://kb.iu.edu/data/acar.html Many folks do the following so that you only need to add a single directory to your path: (a) install all tools in one directory; (b) create a bin directory in the tools directory; (c) use symbolic linking ( http://kb.iu.edu/data/abbe.html ) to link tool executables into the bin directory, e.g., from the bin directory: ln -f -s ../tophat-2.0.8/tophat tophat2 (d) add the bin directory to your path. Good luck, J. On Jun 20, 2013, at 3:34 PM, Jennifer Jackson wrote: Hi Elwood, It sounds like you are getting closer, and that the instructions a few days ago from Jeremy are helping: http://dev.list.galaxyproject.org/transferring-Trapnell-et-al-programs-into-a-one-user-instance-of-Galaxy-tc4660245.html#none For each of these tools in #2, you will need to install them according to the instructions that comes with them from the source. However, there is one change I can mention. Symbolic links pointing from bowtie-bowtie2 and tophat-tophat2 are likely to be present in the default installation. You will want to remove those. Galaxy makes a clear distinction between the versions of the tools. So, you have added tool's as required following the instructions in this wiki: http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies And, in #3, you say that you have started to follow the instructions in this wiki: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies Jeremy also sent you the links about how to obtain and set up the genomes and indexes. Some of this does require limited unix-command line actions and file editing. The instructions are detailed, and some have command lines, because not all, as the exact thing to type can vary. If the line-command is entirely new, I wonder if there is someone locally with unix experience at your site that you can get help from? This last part should not take very long. Best, Jen Galaxy team On 6/20/13 8:45 AM, Elwood Linney wrote: I have: 1) downloaded the Galaxy framework into a Mac Pro desktop with 64gb ram 2) downloaded Mac OS versions of Tophat2, Bowtie2, and the Cufflink suite to the mac 3) have looked at the Galaxy wiki on connecting these [http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies] 4) I have gotten some useful advice from Dannon Baker on how to introduce my large datasets on the some computer into Galaxy through Admin changing some permissions but my minimal knowledge of unix commands and tricks has me stymied Question: If my primary purpose is to use this local instance for the analysis of RNAseq data within my lab, what is the simplest way of connecting the programs to the Galaxy framework? While from reviewing info on the Galaxy website I am only guessing that adding them to $PATH might be the easiest way for me to do this (but I am not exactly sure what this means or specifically how I would do it in my case). However, I do initiate the running of Galaxy by sh run.sh on my terminal and visualizing things via my localhost port. There is some indication from the wiki I found that this might not be good for a system initiated by sh run.sh. [http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies] under Local Jobs I would appreciate any specific advice on this. Sincerely, Elwood Linney DUMC ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] transferring Trapnell et al programs into a one user instance of Galaxy
Elwood, It's not clear what steps you're having problems with, so it's difficult to offer help. Here's the outline that I use to RNA-seq running with Galaxy: *download Samtools, Bowtie2, Tophat2, and the Cufflinks tool suite and add them to my galaxy user's path; *download the iGenomes data package for your genomes: http://cufflinks.cbcb.umd.edu/igenomes.html *configure Galaxy to point to particular data files in iGenomes—specifically, add entries to bowtie2_indices.loc and sam_fa_indices.loc This page will help with this last step: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Let us know if you run into problems. Best, J. On Jun 14, 2013, at 10:31 AM, Elwood Linney wrote: Hello again, I guess I now realize why there is so much traffic on the user list about tools, and I also can guess that while the online directions for dealing with them are written well for those individuals familiar with administration a server or doing full time bioinformatics, but there are some of us computer numbskulls that need something like a Galaxy transfer booklet for computer idiots (biologists) to transfer what we want into a single user or single lab setup. I am hoping there is someone out there like myself who worked through the problem of transferring the Trapnell et al series of programs into a Mac Pro desktop, namely NGS: RNA Analysis 1) Tophat for Illumina tophat (1.3.3-1.4.0) with bowtie + bowtie indexes 2) Cufflinks cufflinks (1.3.0-2.1.1) 3) Cuffcompare cufflinks (1.3.0-2.1.1) 4) Cuffmerge cuffmerge (1.3.0-2.1.1) 5) Cuffdiff cuffdiff (2.1.0-2.1.1) I have transferred the galaxy framework in a work/galaxy-dist pathway unto a solid state drive of a 64gb ram mac that has 3 other 2tb drives and have gotten some valuable advice for transferring large datasets from the same computer via admin. For the next year at least my needs with be just the RNA analysis tools above. Any help will be greatly appreciated. My intention here is remove my contribution to the traffic on the online Galaxy, so some people should consider it a worthy cause Sincerely, Elwood Linney Professor of Molecular Genetics and Microbiology Duke University Medical Cener ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] problem integrating new jar file
You'll need to (a) add an output file to your tool configuration ( see
http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Coutputs.3E_tag_set
) and (b) write your output to the file. See other tool wrappers (e.g.
/tools/filters/cutWrapper.xml) for an example.
Good luck,
J.
On Jun 14, 2013, at 1:07 PM, vijayalakshmi wrote:
Hi,
I am trying to integrate a tool that is written in java into galaxy. The
following is what I've done.
1) Created a directory inside /tools directory and put my xml and runnable
jar file in it.
2) Linked the xml file in 'tool_conf.xml'.
tool_conf.xml
section name=sample tool id=sample_tool
tool file=Sample/sample.xml/
/section
sample.xml
tool id=sample name=Compute correlation
commandjava -jar sample.jar/command
/tool
sample.java (exported into a runnable jar file from eclipse)
package Sample;
public class Sample
{
public static void main(String[] args)
{
System.out.println(Hello world this is important);
}
}
When I run the above, (i.e when I click on execute in the middle pane),
nothing gets added to my current history. Since there is no visual output of
any sort, I am not able to figure out where the problem lies.
Any help or pointer is appreciated!
Thanks y'all!
VJ.
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Re: [galaxy-dev] Download histories
You'll need to wait until the history is ready for download -- i.e., Galaxy provides a .gz file rather than a Webpage at that URL -- before using wget. Galaxy returns a webpage (text/html) while preparing the history for download; this is likely what you are downloading now. Good luck, J. On Jun 13, 2013, at 4:16 PM, Doan, Ryan wrote: Hello, Several people in our lab would like to download all of their histories from their respective Galaxy accounts. We tried to download them using the following steps: Select “Export to File” Copy the provided link and paste into WGet.exe program as follows: wget.exe --no-check-certificate https://main.g2.bx.psu.edu/history/export_archive?id=e0b0f57abd62f2aa -O F:\Galaxy\Ryan\rnd003bucknell.edu\Cattle_seq.galaxy However, we seem to be getting an error on all files from all of their accounts and no files are being saved. See below for cmd prompt output. Resolving main.g2.bx.psu.edu... 128.118.250.4 Connecting to main.g2.bx.psu.edu|128.118.250.4|:443... connected. WARNING: cannot verify main.g2.bx.psu.edu's certificate, issued by `/C=US/O=Inte rnet2/OU=InCommon/CN=InCommon Server CA': Self-signed certificate encountered. WARNING: certificate common name `bigsky.bx.psu.edu' doesn't match requested hos t name `main.g2.bx.psu.edu'. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/html] Saving to: `C:/Users/RDoan/Documents/Lab_Files/Analysis_Programs/Galaxy/test.txt Is this the correct method to download histories or is there a better solution? Thank you for your help! Ryan ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Recently Used Histories
My use case involves working with a lot of histories, and I need to jump back and forth between them fairly frequently. However, it's a bit inconvenient to have to click on the Options button on the rightmost pane, Saved Histories in the drop-down menu, and select my history on the main pane. An easier way to switch between histories that were recently used could definitely benefit me, and perhaps other people too. I propose an easily accessible list with links to the 5 most recently visited histories. This seems useful if implemented well. I envision a drop-down below the 'saved histories' menu item that appears on extended hover and provides links to recent histories. To implement I suggest: (a) create a SQLAlchemy query of user's histories sorted by last update time with limit N (e.g., 5) (b) provide this list to the index.mako template in the root.py/index method (c) refresh the middle frame using handle_refresh_frames() code in message.mako To get started with Galaxy, you'll want to create a fork of galaxy-central and work locally. Once you have something that works, please issue a pull request. Thanks, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff version
Hello, After the latest update of Galaxy I saw that the cuffdiff wrapper is for version 2.0. I updated the $PATH to cuffdiff v. 2.0.2 but when I run cuffdiff in Galaxy I get the following error: Error running cuffdiff. cuffdiff: /lib64/libz.so.1: no version information available (required by cuffdiff) cuffdiff: unrecognized option '--library-norm-method' cuffdiff v1.3.0 (3022) What else do I need to define inorder to run the latest version of cuffdiff. This depends on your setup. If you're running Galaxy under a particular user, you may have to update that user's $PATH. If you're running on a cluster, you'll need to ensure that the submission script uses the correct $PATH. If you provide more details on your set up, it may be possible to provide additional insight/suggestions for your problem. Best, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Trackster set display mode - Output looks all the same
Hi Linda, 1- Should the "Set display mode" give out different output?Not yet.VCF visualization is new to Galaxy, and mode switching isn't implemented yet. (It will be implemented in the next release.)What you're seeing is the display of individual variants; of course, trying to view so many variants leads to the mismash that you noted.If you zoom in sufficiently, you should see variants without trouble. See the attached screenshot for example. 2- What might be the issue if all I see are the same output or maybe the output displayed is totally incorrect? Might there be some trackster setup that I might be missing for it to draw incorrectly?Everything looks OK so far. FYI, I've created a new page that lists the steps for setting up visualization for a Galaxy instance and updated wiki links/text to point to this page:http://wiki.galaxyproject.org/Visualization%20SetupBest,J.___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] problems with exporting or importing data
Anna, Try following these steps: (1) Make your history accessible (Share or Publish -- Make History Accessible by Link). (2) Export your history again; make sure to wait until you can use the URL to download a .gz file of your history. (3) Try importing it via URL to the Huttenhower Lab Galaxy. Let us know if you have any problems. Best, J. On Jun 10, 2013, at 11:45 AM, Edlund, Anna wrote: Hi. I have uploaded fasta files on the main galaxy server through my FileZilla program. In want to transfer them to the Galaxy at the Huttenhower Lab (see http://huttenhower.org/galaxy/root) page and to do that go to history list when I am logged in at both locations and I select ‘Import a History from an archive’. I paste the url address from the main galaxy server (where my archive is located) and select submit. Then I waited for 2 days and nothing was transferred? I am clearly doing something wrong and would really like you input asap. Thank you very much!! Best regards, Anna Edlund My user name is aedl...@jcvi.org ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Trackster error: not able to find the chrom len file
Trackster displays an error after opening a saved view: *** Error: The requested genome file (/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len) could not be opened. Exiting! sort: write failed: standard output: Broken pipe sort: write error Couldn't open /home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len , No such file or directory *** In my universe_wsgi.ini I point to the correct directory where I keep my chrom len files. # Directory where chrom len files are kept, currently mainly used by trackster len_file_path = /mnt/referencedata/trackster This is a bug: Galaxy wasn't using this setting in converters. I've fixed this in -stable changeset 7105c53: https://bitbucket.org/galaxy/galaxy-central/commits/7105c53139d4b8649e6a3714bc117118989712a2 Further, I had to remove the 'chr' in the chrom len files to make it work. This is a problem between the UCSC chromosome naming convention (e.g., 'chr1') and the Ensembl naming convention (e.g. '1'). In most cases Galaxy handles this transparently, but the new converters do not. This is something that definitely needs to be implemented. Here's a card so that you can follow the feature's progress: https://trello.com/c/lai0uU9g Best, J.___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Can I use javascript in the xml to select a date on a calender?
I want to select a date from a calender in my tool, but I think that it's not possible in the xml. Correct, date inputs are not currently implemented in Galaxy parameters. Is this possible? With javascript? Or what? It's possible if you want to extend Galaxy a bit. I suggest (a) adding a DateParameter to Galaxy (probably extending TextToolParameter; see lib/galaxy/tools/parameters/basic.py) and then use the jQueryUI's date picker: http://jqueryui.com/datepicker/ Good luck, J.___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] mapping Summary from Bowtie
how to get the mapping summary from bowtie2 using galaxy interface.. This isn't possible right now, but I've filed a Trello card that you can follow to watch progress on this enhancement: https://trello.com/c/yFeXvhUg Of course, a patch/contribution addressing this issue would be fantastic. Best, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] import Workflow from public Galaxy to local instance
I tracked down this issue to a bug in the workflow export code, and I've fixed it. The fix will appear on our public server early next week; please let us know if you're still seeing this error late next week. Best, J. On May 23, 2013, at 9:50 AM, Andreas Kuntzagk wrote: For the first of the CloudMap workflows that worked. But the second failes with this error message: Failed to open URL: https://main.g2.bx.psu.edu/workflow/export_to_file?id=f444ce954bdc4953 Exception: HTTP Error 500: Internal Server Error I don't see any information in the log files. regards, Andreas On 22.05.2013 13:57, Dannon Baker wrote: On Wed, May 22, 2013 at 3:12 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de mailto:andreas.kuntz...@mdc-berlin.de wrote: But how do I get the workflow_id? For example for the workflow https://main.g2.bx.psu.edu/u/__gm2123/w/cloudmap-unmapped-__mutant-workflow-no-candidates https://main.g2.bx.psu.edu/u/gm2123/w/cloudmap-unmapped-mutant-workflow-no-candidates what would the workflow_id be? (I tried cloudmap-unmapped-mutant-__workflow-no-candidates but this did not work.) If you click on that link above, you can see the id in the url for the 'Import' link. Again, definitely not optimal -- public workflows should probably all be exposed via the API for use/import. -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] cufflinks in the main galaxy instance is not able to produce compatible FPKM score
These are options we'd like to add to Cufflinks, and I've created a Trello card for this enhancement: https://trello.com/c/U7nceKdj I want to add that community contributions via patch or pull request are highly encouraged and are likely to be quicker than waiting for the core team to get to this issue. Best, J. On May 29, 2013, at 8:47 AM, Nikolay N. wrote: Hi, Most people using the RNA-Seq toolkit use a combination of Tophat/Cufflinks/Cuffdiff. A known issue is that cufflinks and cuffdiff use different normalisation schemes (http://seqanswers.com/forums/archive/index.php/t-26041.html). Users overcome this problem by running cufflinks with the following flags: --compatible-hits-norm --max-frag-multihits 1 However, in galaxy it is not possible to run cufflinks with these flags. Can you, perhaps, add support for them? many thanks, Nikolay ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] organizing datasets in the history
When a user creates an account, s/he can create/copy/delete histories and copy datasets from history to history to organize data. Each history, then, is a like a library folder. Best, J. On May 29, 2013, at 11:02 AM, 吳正華 wrote: Hi, galaxy community: I’ve set up a local galaxy for our institute, one thing that our users kept complaining is that when dealing with several dozens of datasets, it became hard to find a certain data. I’m wondering is there a way to organize data in history? Say, organizing datasets in folders just like the file arrangement in the shared data library.. Thank you all for your help. Best Regards, John Wu -- PhD Student Institute of Biomedical Science Academia Sinica ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Displaying genomic sequences in Trackster
Hello! I am trying to enable Trackster on our local galaxy to visualize the mapping results. But, so far, it is not working. Is the twobit.loc file necessary for using Trackster? or is it just optional? Best regards, Menorca Twobit files, configured via twobit.loc, are optional. Here is a page that lists all the steps required to get Galaxy genome visualizations (including Trackster) working: http://wiki.galaxyproject.org/Visualization%20Setup Let us know if you run into any problems or have questions. Thanks, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Samtools and idxstats
Galaxy stores a BAI for each BAM internally; you can access it in a tool
wrapper like this (assuming the name of your input dataset is 'input_bam':
${input_bam.metadata.bam_index}
Once you have the file path, you can set up a symbolic link to it and the tool
should work fine.
Good luck,
J.
On May 22, 2013, at 4:05 AM, Michiel Van Bel wrote:
Hi,
I would like to inquire whether anyone has attempted to implement the
idxstats tool from samtools into Galaxy?
The xml-file for idxstats is not present in the Galaxy source code, which led
me to try and implement it myself.
However, the main problem I face is that the idxstats tool silently relies on
having an index file available (within the same directory) for the bam file
you which to print the stats for.
E.g. samtools idxstats PATH/test.bam
searches for PATH/test.bam.bai and gives an error when this file is not
present. And somehow I cannot model this behavior in Galaxy.
A different solution would of course be to ask the author(s) of samtools to
have an option available where the user can directly indicate the path to the
index file.
regards,
Michiel
PS: I've searched the mailing list archives for this problem but did not find
any matches. Apologies if I somehow missed the answer.
--
==
Michiel Van Bel, PhD
Expert Bioinformatician
Tel:+32 (0)9 331 36 95fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
mi...@psb.vib-ugent.be http://www.psb.vib-ugent.be
http://bioinformatics.psb.ugent.be
==
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Re: [galaxy-dev] Workflow annotations
On the other hand, if a workflow is imported from a file on disk or from a URL, tool level annotations are available while workflow level annotations are not. This has been fixed in this changeset: https://bitbucket.org/galaxy/galaxy-central/commits/8882e45504a3/ Thanks for reporting this issue, J.___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Embedding a help text in a Workflow?
Do you think we could add a new 'rich text' field for a workflow free text help / readme file? Annotations will support HTML, and it's always been the long-term plan that they will include HTML. What's missing is a nice editor for creating HTML annotations. J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] How to transfer or upload datasets to Galaxy server automatically?
You can probably use the API for what you want to do, though your users will need to have an API key to make everything work smoothly. Documentation for the API is here: https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html An alternative approach would be to build a Galaxy data source tool that enables users to get a remote dataset from your site. Here are some information about this approach: http://wiki.galaxyproject.org/Admin/Internals/Data%20Sources Also, check out examples in the GALAXY_HOME/tools/data_source directory. Good luck, J. On May 7, 2013, at 10:54 PM, 王聃Don wrote: Hello, Galaxy developers and maintainers! I'm a user in Chinese mainland and I'd like to deploy our Galaxy server locally. There's some requirements I cannot realize and I still have no idea after searching over all Galaxy Wiki pages and Galaxy Developer docs. The problem is, I need to jump from another external webpage to Galaxy index page through a JS action and a specific included dataset has to be transferred to Galaxy at the same time. In other words, users click a button on an external webpage and will transfer to Galaxy index page with an automatic action of user-login and dataset-uploading in Galaxy server. I've no idea how to realize someway and really need some help on it. Thanks Wang Dan ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Published Workflows missing from All Workflows
i.e. Published Workflows are hidden or separated away from the others. This appears to be a design choice (like shared datasets they must be imported before use), but if so this could be clarified as follows: This was a very old design choice that will be revisited in the (hopefully near) future. I see no reason that published workflows need to be imported before use. J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] List of genomes
You can add genomes in this file: $GALAXYROOT/tool-data/shared/ucsc/builds.txt Note that without related files (e.g. genome sequence, indices for mapping), the build information isn't very useful. However, with an entry in this file, you can link it to other resources when they become available via .loc files: http://wiki.galaxyproject.org/Admin/Data%20Integration Good luck, J. On May 6, 2013, at 11:53 AM, Lee Katz wrote: Hi, I am wondering what I can do to add more genomes to this list (hopefully this image will make it through the mailing list). I am importing fastq files from a MiSeq run. We are using a modified version of Galaxy called Tron. Everything I see on the wiki is about adding custom reference genome assemblies, but I don't understand what to do about adding a species without the reference assembly. Without the correct species, I am forced to use the option unspecified (?) Thanks for your help. image.png -- Lee Katz, Ph.D. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] traceback - local error?
File /mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py, line 1170, in _get_dataset return f, BigWigFile(file=f) File bigwig_file.pyx, line 127, in bx.bbi.bigwig_file.BigWigFile.__init__ (lib/bx/bbi/bigwig_file.c:3011) File bbi_file.pyx, line 119, in bx.bbi.bbi_file.BBIFile.__init__ (lib/bx/bbi/bbi_file.c:3508) File bbi_file.pyx, line 129, in bx.bbi.bbi_file.BBIFile.open (lib/bx/bbi/bbi_file.c:3660) File /mnt/ngswork/galaxy/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg/bx/misc/binary_file.py, line 30, in __init__ if struct.unpack( I, bytes )[0] == magic: error: unpack requires a string argument of length 4 Is this a bug or have I done something unexpected? This looks like an issue in visualizing a wiggle, bedgraph, or bigwig file. Can you provide a dataset to reproduce this issue? Thanks, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tasks (parralelism) and from_work_dir bug
Hi, I have tried to use tasks with tophat2, but I got the following bug. multi.py +153 msg = 'nothing to merge for %s (expected %i files)' \ % (output_file_name, len(task_dirs)) This occurs because tophat2 tool uses from_work_dir feature to get the output files. But on the line: output_files = [ f for f in output_files if os.path.exists(f) ] It returnes an empty list because no real output files exists. Tophat2 cannot be parallelized because it uses a shared junctions database, and shared objects are not yet supported by Galaxy's parallelism. That said, it's likely the case that parallelism + from_work_dir do not work together yet; I've created a card for this issue: https://trello.com/c/5fFZSCWn Best, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] upgrading cufflinks version to 2.0.2
I am trying to upgrade cufflinks version from 1.3.0 to 2.0.2. I changed the directory in the PATH to version 2.0.2 but when I run cuffdiff on the galaxy it still uses the version 1.3.0. Do I need to change the code of the wrapper? This is the right approach, but there must be a glitch somewhere. If you're running Galaxy on a cluster and/or via a dedicated user, you'll want to set the PATH accordingly. For debugging, you could try echoing the path in the tool wrapper. Another question is how to I enable both version of cufflinks to appear and run on the galaxy? This isn't possible now but will be in the future when Cufflinks is moved to the tool shed. Best, J.___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Circster Visualization
But if I click on it I receive an error. Obviously I get this error because I didn't change any file to activate it. Unfortunately, this is not the case. If Trackster works, Circster should work. Can you share the error that you're getting when you click on the Circster icon? Thanks, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Exporting histories fails: no space left on device
Please keep all replies on-list so that everyone can contribute. Someone more knowledgeable about systems than me suggests that lsof(8) and/or /proc/galaxy server pid/fd should yield some clues as to what file is being written to. Good luck, J. On Mar 25, 2013, at 10:01 AM, Joachim Jacob | VIB | wrote: Hi, About the exporting of history, which fails: 1. the preparation seems to work fine: meaning: choosing 'Export this history' in the History menu leads to a URL that reports initially that the export is still in progress. 2. when the export is finished, and I click the download link, the root partition fills and the browser displays Error reading from remote server. A folder ccpp-2013-03-25-14:51:15-27045.new is created in the directory /var/spool/abrt, which fills the root partition. The handler reports in its log: galaxy.jobs DEBUG 2013-03-25 14:38:33,322 (8318) Working directory for job is: /mnt/galaxydb/job_working_directory/008/8318 galaxy.jobs.handler DEBUG 2013-03-25 14:38:33,322 dispatching job 8318 to local runner galaxy.jobs.handler INFO 2013-03-25 14:38:33,368 (8318) Job dispatched galaxy.jobs.runners.local DEBUG 2013-03-25 14:38:33,432 Local runner: starting job 8318 galaxy.jobs.runners.local DEBUG 2013-03-25 14:38:33,572 executing: python /home/galaxy/galaxy-dist/lib/galaxy/tools/imp_exp/export_history.py -G /mnt/galaxytemp/tmpHAEokb/tmpQM6g_R /mnt/galaxytemp/tmpHAEokb/tmpeg7bYF /mnt/galaxytemp/tmpHAEokb/tmpPXJ245 /mnt/galaxydb/files/013/dataset_13993.dat galaxy.jobs.runners.local DEBUG 2013-03-25 14:41:29,420 execution finished: python /home/galaxy/galaxy-dist/lib/galaxy/tools/imp_exp/export_history.py -G /mnt/galaxytemp/tmpHAEokb/tmpQM6g_R /mnt/galaxytemp/tmpHAEokb/tmpeg7bYF /mnt/galaxytemp/tmpHAEokb/tmpPXJ245 /mnt/galaxydb/files/013/dataset_13993.dat galaxy.jobs DEBUG 2013-03-25 14:41:29,476 Tool did not define exit code or stdio handling; checking stderr for success galaxy.tools DEBUG 2013-03-25 14:41:29,530 Error opening galaxy.json file: [Errno 2] No such file or directory: '/mnt/galaxydb/job_working_directory/008/8318/galaxy.json' galaxy.jobs DEBUG 2013-03-25 14:41:29,555 job 8318 ended The system reports: Mar 25 14:51:26 galaxy abrt[16805]: Write error: No space left on device Mar 25 14:51:27 galaxy abrt[16805]: Error writing '/var/spool/abrt/ccpp-2013-03-25-14:51:15-27045.new/coredump' Thanks, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On Tue 19 Mar 2013 11:22:27 PM CET, Jeremy Goecks wrote: I'm unable to reproduce this behavior using a clean version of galaxy-dist. The code (export_history.py) doesn't create any temporary files and appears to write directly to the output file, so it seems unlikely that Galaxy is writing anything to the root directory. Can you provide the name of any file that Galaxy appears to be writing to outside of galaxy-home? What about watching the job output file/export file to see if that's increasingly in size and causing the out-of-space error? Best, J. On Mar 19, 2013, at 10:56 AM, Joachim Jacob | VIB | wrote: Hi all, Exporting histories fails on our server: Reason: *Error reading from remote server. *When looking at the logs and the system: tail /var/log/messages Mar 19 15:52:47 galaxy abrt[25605]: Write error: No space left on device Mar 19 15:52:49 galaxy abrt[25605]: Error writing '/var/spool/abrt/ccpp-2013-03-19-15:52:37-13394.new/coredump' So I watched my system when I repeated the export, and saw that Galaxy fills up the root directory (/), instead of any temporary directory. Somebody has an idea where to adjust this setting, so the export function uses any temporary directory? Thanks, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] user-specific tool panel
Jens, This isn't possible right now but has been suggested in the past. I've created a Trello card for the idea that you can comment/vote on: https://trello.com/c/zQcLM6I4 Best, J. On Mar 22, 2013, at 6:04 AM, Keilwagen, Jens wrote: Hi guys, I'm wondering whether it is possible to have user-specific tool panels after logging in. This way users could customize the tool panel for instance by increasing the visibility of their (user-specific) favorites ... This would be a wonderful feature. However searching in the documentation and the mailing list, I did not find anything. Hence, it would be great if anybody could give me a hint or if impossible to mark this as a feature request. Thanks for any help. Jens ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Issue with viz of mapped data in Trackster
Indeed, following error occurs: 157.193.10.150 - - [19/Mar/2013:08:30:06 +0200] GET /visualization/trackster HTTP/1.1 200 - http://galaxy.bits.vib.be/; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.22+ (KHTML, like Gecko) Chromium/17.0.963.56 Chrome/17.0.963.56 Safari/535.22+ galaxy.webapps.galaxy.api.datasets ERROR 2013-03-19 08:30:13,722 Error in dataset API at listing contents: : Traceback (most recent call last): File /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py, line 41, in show is_true( kwd.get( 'retry', False ) ) ) File /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py, line 96, in _converted_datasets_state if not data_provider.has_data( chrom ): File /home/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py, line 814, in has_data st = summary_tree_from_file( self.converted_dataset.file_name ) File /home/galaxy/galaxy-dist/lib/galaxy/visualization/tracks/summary.py, line 114, in summary_tree_from_file st = cPickle.load( st_file ) EOFError This is the error that occurs when trying to read a dataset's index. What you want to look for is the error that occurs when creating this index; you'll need to look in the database to find this error. Here's a SQL command that will look for the most recent summary tree converter jobs: -- select * from job where tool_id like 'CONVERTER%summary_tree%' order by id desc; -- Is there anything in standard out/error that would explain why the summary tree is not created? I have found the root cause I believe: when I visualize datasets from a data library, the data is not displayed. Getting them from the source history gets displayed is OK Importing them from a data library in a history, and displaying in trackster works I cannot reproduce this on a clean version of galaxy-dist. One guess is library permissions may be causing a problem. Are the datasets that you want to visualize in a library (or they themselves) under restricted access? Thanks, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Exporting histories fails: no space left on device
I'm unable to reproduce this behavior using a clean version of galaxy-dist. The code (export_history.py) doesn't create any temporary files and appears to write directly to the output file, so it seems unlikely that Galaxy is writing anything to the root directory. Can you provide the name of any file that Galaxy appears to be writing to outside of galaxy-home? What about watching the job output file/export file to see if that's increasingly in size and causing the out-of-space error? Best, J. On Mar 19, 2013, at 10:56 AM, Joachim Jacob | VIB | wrote: Hi all, Exporting histories fails on our server: Reason: *Error reading from remote server. *When looking at the logs and the system: tail /var/log/messages Mar 19 15:52:47 galaxy abrt[25605]: Write error: No space left on device Mar 19 15:52:49 galaxy abrt[25605]: Error writing '/var/spool/abrt/ccpp-2013-03-19-15:52:37-13394.new/coredump' So I watched my system when I repeated the export, and saw that Galaxy fills up the root directory (/), instead of any temporary directory. Somebody has an idea where to adjust this setting, so the export function uses any temporary directory? Thanks, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Issue with viz of mapped data in Trackster
It's likely that the job creating the summary tree failed for some reason. Can you please look through your database for summary tree jobs and see if they have any standard out/err that could provide insight into the problem? Thanks, J. On Mar 15, 2013, at 9:47 AM, Joachim Jacob | VIB | wrote: Hi all, Since the last updata of Galaxy, I was not able anymore to view newly added tracks to existing or newly created visualisations. In the webhandler, I have traced down this error: 193.191.128.2 - - [14/Mar/2013:11:02:13 +0200] GET /api/datasets/407a09c0b5976b4e?hda_ldda=hdadata_type=converted_datasets_statechrom=chr4 HTTP/1.1 500 - http://galaxy.bits.vib.be/visualization/trackster?id=1ec2297821c7f2cb; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.22+ (KHTML, like Gecko) Chromium/17.0.963.56 Chrome/17.0.963.56 Safari/535.22+ galaxy.webapps.galaxy.api.datasets ERROR 2013-03-14 11:03:02,409 Error in dataset API at listing contents: : Traceback (most recent call last): File /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py, line 41, in show is_true( kwd.get( 'retry', False ) ) ) File /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py, line 96, in _converted_datasets_state if not data_provider.has_data( chrom ): File /home/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py, line 814, in has_data st = summary_tree_from_file( self.converted_dataset.file_name ) File /home/galaxy/galaxy-dist/lib/galaxy/visualization/tracks/summary.py, line 114, in summary_tree_from_file st = cPickle.load( st_file ) EOFError Thanks for any assistance, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
