Re: [galaxy-dev] adding IDR to Amazon AMI
Hi Quang, We have no immediate plans to extend the toolset of the tools available on the default image so I'd suggest one of two options to get this tool out: 1. Create a Galaxy Tool wrapper for it and upload it to the Tool Shed at http://toolshed.g2.bx.psu.edu/ 2. Install it on an Galaxy CloudMan instance and use the 'share-a-cluster' feature to make a copy of the entire instance available to others Hope this helps, Enis On Sun, Jun 17, 2012 at 10:04 AM, Quang Trinh quang.tr...@gmail.com wrote: Hi dev, Just wondering if there is plan to add IDR ( please see the link below ) to Galaxy Amazon AMI? https://sites.google.com/site/anshulkundaje/projects/idr IDR is being used by both modENCODE and ENCODE projects for ChiP-seq analysis. Thanks, Q ___ 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] Configuring Proftpd for galaxy.
Hi, Thank you very much for your reply. I have tried it and i got 504 and 504. So i must replace in this line: LookupGalaxyUser SELECT email,password,'504','504','/home/nate/galaxy_dist/database/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U' Best regards Mish Date: Fri, 15 Jun 2012 15:55:02 +0200 From: geert.vandewey...@ua.ac.be To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Configuring Proftpd for galaxy. 512 is the unix UID (userid) and GID (groupid) of the user running the galaxy daemon. This should be adapted to meet your situation. in our case it is 1009 and 100 for example. Look it up using : $ id **the username running galaxy** best regards Geert Vandeweyer On 06/15/2012 03:35 PM, Misharl mon wrote: Hi everybody, I'm configuring Proftpd so that it can work with Galaxy installed in a cluster. I don't understand why for the UID and GID, it has been chosen the number 512? # Define a custom query for lookup that returns a passwd-like entry. UID and GID should match your Galaxy user. SQLUserInfo custom:/LookupGalaxyUser138.102.49.9 SQLNamedQuery LookupGalaxyUser SELECT email,password,'512','512','/home/nate/galaxy_dist/database/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U' Because, when a galaxy user tries to connect via filezilla to upload files, the Proftpd server 's logs shows:chdir (/work/...): Permission denied . I think i have a problem with the UID and GID which doesn't match somehow? Thanks in advance to all. Mish -- ___ 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/ -- 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/pub/geert-vandeweyer/26/457/726 ___ 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] Configuring Data Library Usage for Non-Admins
Okay, so the only way for a user to upload a file with a size greater than 2GB is to use FTP? Or can a non-admin user be granted permission to upload files using the filesystem path option, given that he/she can only access his/her own directory? Thanks, CL ___ 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] adding tools using toolshed is not working
Hi Greg, Thanks a lot. This solved the issues I had. Greetz, Mattias On 06/15/2012 04:28 PM, Greg Von Kuster wrote: Hi Matthias, You uncovered an issue I recently introduced and which I've fixed in change set 7277:4a1389e037c6, which is now running on both public Galaxy tool sheds. Sorry for the back and forth on this - your line numbers in your paster log threw me since they were significantly different from mine. Thanks for reporting this problem! Greg Von Kuster On 06/15/2012 02:58 PM, Greg Von Kuster wrote: Hi Matthias, There is really nothing to configure in your Galaxy environment in order to use the public Galaxy tool sheds. Ideally, you should set the following configuration setting, but not setting it defaults to using the file named shed_tool_conf.xml for installed tools anyway. tool_config_files = tool_conf.xml,shed_tool_conf.xml The current Galaxy central repository tip is 7276:622fd4f0a437, which you should pull. This is the revision that the public tool sheds are using - they generally always run the Galaxy central tip revision. It's very possible that since you updated after 6 months of development, your repository has some issues. What are the results of the following commands? hg diff hg status hg verify hg summary On Jun 15, 2012, at 7:55 AM, Hollander, Mattias de wrote: Hi Greg, I guess something went wrong while update, because I updated to the latest changeset: hg tip | grep changeset changeset: 7262:4fbd05095ca7 Can it be because I the last time I updated was at least half a year ago and the toolshed integration has been implemented afterwards? So that I need to configure the toolshed before I can install something form the public one? Thanks! Mattias On 06/13/2012 05:43 PM, Greg Von Kuster wrote: Hello Mattias, Did you pull from the Galaxy central repo? The latest change set is 7262:4fbd05095ca7, which is what you should be running in order to use the tool shed. Let me know if you in fact have the latest from central - your line numbers in your log below look to be different from mine. Thanks, Greg Von Kuster On Jun 13, 2012, at 11:38 AM, Hollander, Mattias de wrote: Hi, I just updated my local Galaxy installation to the latest version. I am trying out the feature to add tools directly from the toolshed, but this is not working. It results in this error: File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/exceptions/errormiddleware.py', line 144 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', line 106 in __call__ environ, self.app) File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', line 543 in intercept_output app_iter = application(environ, replacement_start_response) File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/__init__.py', line 184 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxyTools/galaxy-central/lib/galaxy/web/controllers/admin_toolshed.py', line 481 in install_repository install_tool_dependencies=install_tool_dependencies ) File '/home/galaxyTools/galaxy-central/lib/galaxy/util/shed_util.py', line 1228 in load_repository_contents dist_to_shed=False ) File '/home/galaxyTools/galaxy-central/lib/galaxy/util/shed_util.py', line 342 in create_or_update_tool_shed_repository installed_changeset_revision=changeset_revision, NameError: global name 'changeset_revision' is not defined And my shed_tools_conf.xml looks like this: ?xml version=1.0? toolbox tool_path=../shed_tools /toolbox Should I put more configuration in this file? Any help is appreciated. Thanks! Mattias ___ 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/
[galaxy-dev] Citations for tools
Hi all, I'd like to suggest, or request, a feature - I think that posting to galaxy-dev is the right place to start? After I've done an analysis, it would be useful to be given a list of references for all the tools I used in that history, which I could use to cite the appropriate papers. At the moment, it seems that most tool developers add a please cite the following paper note to the help tag in the wrapper so that it displays on the tool screen before you run it. I'd like to suggest: * adding a cite tag to the tool wrappers xml, * adding a feature to the history UI which will list all the references to cite for the a history. I think this would encourage people to cite the tools they use properly and hence encourage developers to put their tools into the toolshed! With the standard tools moving into the toolshed it will be really important for tool wrappers to be maintained. Any thoughts? Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___ 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] Citations for tools
On Mon, Jun 18, 2012 at 10:29 AM, Clare Sloggett s...@unimelb.edu.au wrote: Hi all, I'd like to suggest, or request, a feature - I think that posting to galaxy-dev is the right place to start? After I've done an analysis, it would be useful to be given a list of references for all the tools I used in that history, which I could use to cite the appropriate papers. At the moment, it seems that most tool developers add a please cite the following paper note to the help tag in the wrapper so that it displays on the tool screen before you run it. I'd like to suggest: * adding a cite tag to the tool wrappers xml, * adding a feature to the history UI which will list all the references to cite for the a history. I think this would encourage people to cite the tools they use properly and hence encourage developers to put their tools into the toolshed! With the standard tools moving into the toolshed it will be really important for tool wrappers to be maintained. Any thoughts? Clare Hi Clare, We talked about this at the end of last year, and yes, it would be a good idea: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007873.html Are you familiar enough with the area of semantic web/linked data to know what would be the best XML based markup to use for embedding the citations? 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/
[galaxy-dev] Bug report - when trying to use Bam and Bai files
Hello all,
I have a problem with Galaxy, and until now I haven't found a solution for it.
We have a tool that has two inputs: one BAM file and one BAI file. The BAI file
is the index of this BAM file.
I noticed that when there is a needed for BAI file of some BAM file, Galaxy
first generate a BAI dataset from the BAM, and then sends those two inputs to
this tool.
Until now, everything works perfect.
The problem is occurred when as part of some workflow, there is a pre-step that
create the BAM file, and the step after it need this BAM and also its BAI.
In this case, the second step is failed and I get this error massage:
input data 55 (file: {path}/dataset_1547.dat) was deleted before the job
started
As part of the debugging process, I monitored this workflow execution,
and I noted that Galaxy tried to execute the second step BEFOR the BAi files
has generated, and therefore this job is doomed to failure ...
After a few seconds, when the job has already failed, the BAI file is
generated... but of course, it is too late :(
Any help will be appreciated!
Thanks,
Liram
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[galaxy-dev] adding IDR to Galaxy
Hi dev, Just wondering if there is plan to add IDR ( please see the link below ) to Galaxy Amazon AMI? https://sites.google.com/site/anshulkundaje/projects/idr IDR is being used by both modENCODE and ENCODE projects for ChiP-seq analysis. Thanks, Q ___ 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] Configuring Data Library Usage for Non-Admins
On Jun 18, 2012, at 5:04 AM, Ciara Ledero wrote: Okay, so the only way for a user to upload a file with a size greater than 2GB is to use FTP? Or can a non-admin user be granted permission to upload files using the filesystem path option, given that he/she can only access his/her own directory? Hi Ciara, They can use the upload from a directory method if you configure Galaxy as explained by greg (user_library_import_dir). Users will also need to have permissions to upload to libraries that the admin chooses. From the admin interface, select a library, click Library Actions - Edit permissions, and then assign the appropriate users' private role(s) to the add library item permission. --nate Thanks, CL ___ 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/
[galaxy-dev] Column alignment in tabular display
Hello all,
I'm curious about the logic used for column alignment when displaying
tabular files (which for me was the headline feature of the last
Galaxy Release - I'm very pleased to have this added at last).
https://bitbucket.org/galaxy/galaxy-central/issue/553
Quoting from templates/dataset/tabular_chunked.mako
function renderCell(cell_contents, index, colspan){
if (colspan !== undefined){
return $('td').attr('colspan',
colspan).addClass('stringalign').text(cell_contents);
}
else if (DATASET_TYPES[index] == 'str'){
/* Left align all str columns, right align the rest */
return $('td').addClass('stringalign').text(cell_contents);;
}
else{
return $('td').text(cell_contents);
}
}
It seems to me that the logic should be right align all numeric
columns, left align the rest. At very least, columns of type 'list'
should also be left aligned. Otherwise you can easily have a situation
where on clicking the eye you get an apparently empty dataset
(unless you scroll right or down).
This can easily happen with FASTA to tabular (default settings), where
the descriptions have commas in them (common with annotation) thus the
first column is considered to be a list (and the second column type
str for the sequence). If some of the later sequences in the file have
very long descriptions, right aligning the description column makes
the dataset appear empty.
I can provide a screen shot if it would help to explain, but here is
my proposed patch.
Regards,
Peter
--
$ hg diff templates/dataset/tabular_chunked.mako
diff -r 8657ada96fca templates/dataset/tabular_chunked.mako
--- a/templates/dataset/tabular_chunked.makoFri Jun 15 16:05:48 2012 +0100
+++ b/templates/dataset/tabular_chunked.makoMon Jun 18 16:23:44 2012 +0100
@@ -17,8 +17,8 @@
if (colspan !== undefined){
return $('td').attr('colspan',
colspan).addClass('stringalign').text(cell_contents);
}
-else if (DATASET_TYPES[index] == 'str'){
-/* Left align all str columns, right align the rest */
+else if (DATASET_TYPES[index] == 'str' ||
DATASET_TYPES[index] == 'list'){
+/* Left align all str and list columns, right align the rest */
return $('td').addClass('stringalign').text(cell_contents);;
}
else{
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Re: [galaxy-dev] tool_data_table_config.xml.sample
Hi Birgit, Did you upload the same tarball you sent me previously, or was it a different tarball. If different, can you send it to me? Thanks On Jun 18, 2012, at 8:18 PM, Birgit Crain wrote: Hi Greg I just created a repository on the main toolshed and upload a tar ball. I got the same error messages again as described in the email thread below. Regards Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete Genomics, Inc. (650) 428-6023 office | (408) 605-3938 mobile bcr...@completegenomics.com From: Greg Von Kuster g...@bx.psu.edu Date: Thursday, June 14, 2012 11:44 AM To: Birgit Crain bcr...@completegenomics.com Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] tool_data_table_config.xml.sample Hello Birgit, This issue has been resolved in changeset 7272:b761471d7590, which is currently available from our Galaxy central repository. Both the Galaxy test and Galaxy main tool sheds are running this latest changeset revision. Thanks very much for reporting this problem! Greg Von Kuster On Jun 14, 2012, at 12:45 PM, Birgit Crain wrote: Hi Greg I was using the Galaxy test toolshed to upload the files into a repository. On my Mac where I develop the tools I have a local instance that I loaded from zipped file (downloaded April galaxy-galaxy-dist-40f1816d6857.zip) running python 2.7. When I download the repository to a local instance on our server the tools and .loc file install fine (except that I don't have my datatypes defined right, working on that). Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete Genomics, Inc. (650) 428-6023 office | (408) 605-3938 mobile bcr...@completegenomics.com From: Greg Von Kuster g...@bx.psu.edu Date: Wednesday, June 13, 2012 6:05 PM To: Birgit Crain bcr...@completegenomics.com Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] tool_data_table_config.xml.sample Hi Birgit, What version of Galaxy are you running? You can determine this by typing hg heads in your Galaxy installation directory. Also, what version of Python are you running, and what database are you using? Can you also provide the complete paster log from you tool shed? Thanks, Greg Von Kuster On Jun 13, 2012, at 6:13 PM, Birgit Crain wrote: Hi Greg Thanks for the tip. The .file items appear when I tar the directory on my Mac, so I work around that issue and tar the directory on a UNIX server. Thus said I happily did the same with another directory that contains tools that are all dependent on the tool_data_table_conf.xml.sample and the tool-data/cg_crr_files.loc.sample file. This directory has the following files: cgatools/README.txt cgatools/tool_data_table_conf.xml.sample cgatools/datatypes_conf.xml cgatools/lib/galaxy/datatypes/completegenomics.py cgatools/tool-data/cg_crr_files.loc.sample cgatools/tools/cg_cgatools/listvariants.xml cgatools/tools/cg_cgatools/junctiondiff.xml cgatools/tools/cg_cgatools/snpdiff.xml cgatools/tools/cg_cgatools/calldiff.xml cgatools/tools/cg_cgatools/testvariants.xml cgatools/tools/cg_cgatools/varfilter.xml cgatools/tools/cg_cgatools/listtestvariants.xml cgatools/tools/cg_cgatools/join.xml cgatools/tools/cg_cgatools/varfilter_wrapper.pl When I upload this tar ball to the repository, one tool, calldiff, which is alphabetically the first one in the list, loads properly and for the others I get the following error message: Metadata was defined for some items in revision 'e183f52194a5'. Correct the following problems if necessary and reset metadata. join.xml - This file refers to a missing file cg_crr_files.loc. Upload a file named cg_crr_files.loc.sample to the repository to correct this error. junctiondiff.xml - This file refers to a missing file cg_crr_files.loc. Upload a file named cg_crr_files.loc.sample to the repository to correct this error. listtestvariants.xml - This file refers to a missing file cg_crr_files.loc. Upload a file named cg_crr_files.loc.sample to the repository to correct this error. listvariants.xml - This file refers to a missing file cg_crr_files.loc. Upload a file named cg_crr_files.loc.sample to the repository to correct this error. snpdiff.xml - This file refers to a missing file cg_crr_files.loc. Upload a file named cg_crr_files.loc.sample to the repository to correct this error. testvariants.xml - This file refers to a missing file cg_crr_files.loc. Upload a file named cg_crr_files.loc.sample to the repository to correct this error. varfilter.xml - This file refers to a missing file cg_crr_files.loc. Upload a file named cg_crr_files.loc.sample to the repository to correct this error. For the invalid tools is show this explanation: [Errno 2] No such file or directory: '/var/opt/galaxy/g2cmnty/tmp/work_tmp/cg_crr_files.loc' But I know the file is there …. Any
[galaxy-dev] Index files for bfast
Hello all, I have been trying to fix the index problem of BFast since last week, somehow, the index didn't show in the drop-down box no matter how I managed to modify the configurations. I listed my steps in the following, hopefully you can help me to point out where the problem is: Taken one example for Ecoli. The index files plus a symbolic link of the genome file for Bfast are stored in == /galaxyIndices/genomes/Ecoli/eschColi_K12/bfast I check the global conf files, tool_conf.xml and tool_data_table_conf.xml, which both contain the relevant files (sr_mapping/bfast_wrapper.xml and tool-data/bfast_indexes.loc) for bfast. The index should be displayed through the following codes in tools/sr_mapping/bfast_wrapper.xml: when value=indexed param name=indices type=select label=Select a reference genome options from_data_table=bfast_indexes filter type=multiple_splitter column=2 separator=,/ filter type=param_value column=2 ref=input1 ref_attribute=extension/ filter type=sort_by column=3/ validator type=no_options message=No indexes are available for the selected input dataset/ /options /param /when And the bfast_indexes == tool-data/bfast_indexes.loc, which points to the directories where the index files are: #unique_idbuild galaxy format extensions valid1,valid2 description bfast_index_directory eschColi_K12eschColi_K12 fastqsanger,fastqcssanger eschColi_K12 /galaxyIndices/genomes/Ecoli/eschColi_K12/bfast/eschColi_K12.fa Any suggestions? Look forward to your reply. Best regards, Sean ___ 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/
