[galaxy-dev] FTP Problem: Users cannot see their uploads files.
Hi everybody, I have managed to get proftpd to work, it can connect to the galaxy sql database, and users can log to upload files in their directory. But there is a problem, when a galaxy user logs in the galaxy web platform, the user can't see his upload files since Galaxy doesn't have the rights to open the directory. How can i change the permissions in proftpd so that galaxy can open the user directory? 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/
Re: [galaxy-dev] Error when exporting history to file
Hi Jeremy, I'm using galaxy-dist, but it's quite possible that I'm a version or two behind. I'm not yet able to reproduce the problem on the public server, but I'm still missing some steps from the input to the problematic dataset. I'll get back to you if I'm able to reproduce it or if it still persist when I have updated our Galaxy server. Thanks for your help! Best regards, Sarah On 05/09/2012 02:09 AM, Jeremy Goecks wrote: Sarah, I'm not able to reproduce your issue using galaxy-central. This could mean that this bug has been fixed in galaxy-central but hasn't made it to galaxy-dist yet—it appears you are using galaxy-dist—or there's other information needed to reproduce this issue. A couple more questions: Are you using galaxy-dist? Can you reproduce the issue on our public server using the problematic dataset and/or workflow? Thanks, J. On May 7, 2012, at 12:33 PM, Sarah Diehl wrote: Sort (version 1.0.1) on column: c5 with flavor: Numerical sort everything in: Descending order On 05/07/2012 06:28 PM, Jeremy Goecks wrote: Sarah, What tool was used to create the problematic dataset? Thanks, J. On May 7, 2012, at 12:17 PM, Sarah Diehl wrote: Hi all, I get the following error when I try to export a specific history to file: 10.1.5.190 - - [07/May/2012:18:01:08 +0200] GET /history/export_archive HTTP/1.1 500 - http://galaxy.immunbio.mpg.de/; Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.24) Gecko/2008 Fedora/3.6.24-1.fc14 Firefox/3.6.24 Error -type 'exceptions.TypeError':galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0 is not JSON serializable URL: http://galaxy.immunbio.mpg.de/history/export_archive File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/history.py', line 678 in export_archive history_exp_tool.execute( trans, incoming = params, set_output_hid = True ) File '/galaxy/galaxy_server/lib/galaxy/tools/__init__.py', line 1517 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/tools/actions/history_imp_exp.py', line 106 in execute include_deleted=incoming[ 'include_deleted' ] ) File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 428 in setup_job jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py', line 268 in dumps File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 214 in encode File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 282 in iterencode File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 327 in default return simplejson.JSONEncoder.default( self, obj ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 190 in default TypeError:galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0 is not JSON serializable I tracked the problem down to a single bed file. I copied it into a new empty history and I can still not export this history to a file. This file doesn't have any special characters in either its name, info or annotation. I can't find anything special about this file... Any help is greatly appreciated! Best regards, Sarah ___ 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/ ___ 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] MarkupSafe cannot be fetched
Hello, To solve this warning, python used by Galaxy is now localized on our server. I no longer use python available on our cluster. Thus, if python version on the cluster evolves, it will not impact Galaxy. Thanks to this modification, your script fetch_eggs.py have been start and some eggs have been updated except for Markupsafe. So I downloaded Markupsafe from Python website. Since then I have no warning on my runs ;-) Thanks, Sarah Nate Coraor a écrit : On Apr 27, 2012, at 6:00 AM, Sarah Maman wrote: Hello, After pulling latest changes (March 2012 - r 40f1816d6857), jobs launched run properly (output files OK) but I get the following warning: /WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched/ Hi Sarah, I'm guessing that you are using a cluster with Galaxy. If this is correct, please try the following: 1. Log in to a cluster node as the user that runs Galaxy 2. cd to the galaxy-dist directory 3. run `python ./scripts/fetch_eggs.py` This should grab any missing eggs. In addition, Galaxy GUI is not exactly GUI seen in the cloud (https://main.g2.bx.psu.edu/). For example, Visualization menu is absent and I think it should be related to the previous warning? See the 'enable_tracks' setting in universe_wsgi.ini to enable the Visualization menu. --nate How to ensure that eggs be properly fetched? Thank you in advance, Sarah Maman ___ 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] MPileup reference genome bug?
I am generating a pileup of BAM data from the 1000 genomes project using MPileup. I have associated the BAM file with the hg19 genome, but every single reference base in the output appears as an N. Is there some extra step I have to perform when using a BAM file that was not generated from within Galaxy? Many thanks, luce ___ 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] Sub-task splitting
On 12-05-03 9:51 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hello all, Currently the Galaxy experimental task splitting code allows splitting into N chunks, e.g. 8 parts, ... Or, into chunks of at most size N (units dependent on the file type, e.g. lines in a tabular file or number of sequences in FASTA/FASTQ), e.g. at most 1000 sequences: ... I would prefer to be able to set both sizes - in this case tell Galaxy to try to use at least 8 parts, each of at most 1000 sequences. ... Does this sound sufficiently general? The split code is still rather experimental so I don't expect breaking the API to be a big issue (not many people are using it). Peter On Thu, May 3, 2012 at 6:01 PM, Paul Gordon gord...@ucalgary.ca wrote: +1. This is especially useful for us, with hardware-accelerated algorithms having limits on input size. I've got this working with FASTA files on our Galaxy at the moment, and touch-wood it is behaving nicely. The code doesn't yet handle splitting other input file formats, which would be required before applying this to the trunk - but some feedback on if the Galaxy team are keen on this direction or not would be appreciated: https://bitbucket.org/peterjc/galaxy-central/changeset/aa98de8effd1 (I'll have to sort out the branches since this is now mixed up with BLAST database work... but that is an aside). 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/
Re: [galaxy-dev] FTP Problem: Users cannot see their uploads
Hi Mish, In the proftpd.conf file, do you have the user and group fields set to your Galaxy user and group? Let me know if the question needs further clarification. Thanks, Dan Message: 10 Date: Wed, 9 May 2012 08:21:19 + From: Misharl mon mish...@hotmail.com To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] FTP Problem: Users cannot see their uploads files. Message-ID: dub106-w582aaf4ad01bfb3e1d1069af...@phx.gbl Content-Type: text/plain; charset=iso-8859-1 Hi everybody, I have managed to get proftpd to work, it can connect to the galaxy sql database, and users can log to upload files in their directory. But there is a problem, when a galaxy user logs in the galaxy web platform, the user can't see his upload files since Galaxy doesn't have the rights to open the directory. How can i change the permissions in proftpd so that galaxy can open the user directory? 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/
Re: [galaxy-dev] Loc file configuration question
Hi Jen, Thank you for your response. I seem to have all the relevant entries in the two *.loc files you mentioned (paths in all_fasta files and the twobit files are different because of the way we have the files stored. I also converted the 2bit files to .fa and have them available in the same twobit directory). But the feature extraction is still not working. Here are the relevant entries in files (I have redacted specific file paths and replaced them with path_to): twobit.loc hg18/path_to/twobit/hg18.2bit hg19/path_to/twobit/hg19.2bit mm9/path_to/twobit/mm9.2bit mm8/path_to/twobit/mm8.2bit all_fasta.loc hg19fullhg19Human (Homo sapiens): hg19 Full /path_to/hg19/bwa_path/hg19_all.fa hg19_chr_only hg19_chrHuman (Homo sapiens): hg19_chrom_only /path_to/hg19/bwa_path/hg19.fa hg18fullhg18Human (Homo sapiens): hg18 Full /path_to/hg18/bwa_path/hg18_all.fa hg18_chr_only hg18_chrHuman (Homo sapiens): hg18_chrom_only /path_to/hg18/bwa_path/hg18_chrom_only.fa I assume that the second field in the (all_fasta.loc) file dbkey has to match the builds.txt file in the ucsc directory. Is that correct? It does in this case. I think I am missing something subtle here. The *.loc.sample files are great but the information contained in those is confusing. I am not sure why there are two examples of the same info (as far as I can tell) in most sample loc files. Thanks. On Tue, May 8, 2012 at 6:48 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Raja, This tool uses a database.2bit file to extract sequence data when the 'Locally cashed' option is used. The database is a genome that you install locally. .2bit format was developed by UCSC and they are the source for many genomes in this format already and for tools (compiled and uncompiled) to transform fasta data into/from .2bit format (faTwoToBit and twoBitToFa): http://hgdownload.cse.ucsc.**edu/downloads.htmlhttp://hgdownload.cse.ucsc.edu/downloads.html(genomes + source) http://hgdownload.cse.ucsc.**edu/admin/exe/linux.x86_64/http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/(compiled utilities) For the extract tool, the builds list is required: http://wiki.g2.bx.psu.edu/**Admin/Data%20Integrationhttp://wiki.g2.bx.psu.edu/Admin/Data%20Integration You don't actually need to have more NGS set up beyond that. Still, this wiki can help. http://wiki.g2.bx.psu.edu/**Admin/NGS%20Local%20Setuphttp://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup For example, the database.2bit file could be placed with your .fa files like: /galaxy-dist/tool-data/genome/**databaseA/seq/databaseA.**2bit /galaxy-dist/tool-data/genome/**databaseA/seq/databaseA.fa /galaxy-dist/tool-data/genome/**databaseB/bowtie/ /galaxy-dist/tool-data/genome/**databaseB/sam/ /galaxy-dist/tool-data/genome/**databaseB/seq/databaseB.**2bit /galaxy-dist/tool-data/genome/**databaseB/seq/databaseB.fa /galaxy-dist/tool-data/genome/**databaseC/seq/databaseC.**2bit /galaxy-dist/tool-data/genome/**databaseC/seq/databaseC.fa /galaxy-dist/tool-data/genome/**databaseD/seq/databaseD.**2bit /galaxy-dist/tool-data/genome/**databaseD/seq/databaseD.fa Then the .loc file is here: /galaxy-dist/tool-data/twobit.**loc.sample You will probably have this for all genomes as well: /galaxy-dist/tool-data/all_**fasta.loc.sample Remove the .sample before using these. Instructions for how to populate each are in the files themselves. The only gtf/gff files associated with this tool would be datasets from the history, so there are no gtf/gff data to stage before using the tool. To have the tool use a particular genome, set the query dataset (interval, bed, gtf) to have the same database identifier as you used for the database part of the database.2bit file. (This is why the builds list is required). If you make changes to data, don't forget to restart your server to see the changes. Hopefully this helps, Jen Galaxy team On 5/8/12 12:46 PM, Raja Kelkar wrote: I have two questions that pertain to a local install of galaxy: 1. I have been having trouble getting the “fetch sequences” à “extract genomic DNA” tool to work. Can someone identify the specific *.loc file that needs to have the info about the location of the genome sequence files? I get the following error when I run the extract tool: /No sequences are available for 'hg19’, request them by reporting this error./ // 2. What configuration file(s) need to contain locations for the gtf/gff files? Thanks. __**_ 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/ -- Jennifer Jackson http://galaxyproject.org ___ Please keep all replies on the list by using reply all in your mail
Re: [galaxy-dev] [galaxy-user] Help on installing cutadapt
Hi Jen, Thank you for the suggestions. I did try to log in to Galaxy under User --Login. The password is the one I use for the Galaxy Main. However, it gives me the error message No such user (please note that login is case sensitive). I do not see a place to set Admin password in the universe_wsgi.ini file. Here is how I setup the Admin permissions under Users and Security in the universe_wsgi.ini file: 1. id_secrete = gave a mix of numbers and letters 2. use_remote_user = True 3. remote_user_maildomain = tilahun.ab...@uni.edu 4. remote_user_logout_href = None 5. Admin_users = tilahun.ab...@uni.edu 6. require_login = True 7. allow_user_creation = False 8. allow_user_deletion = True 9. allow_user_impersonation = True 10. allow_user_dataset_purge = True 11. new_user_dataset_access_role_default_private = True Can you check and let me know information I missed? Thanks. Tilahun -- On Tue, May 8, 2012 at 4:53 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hello Tilahun, Are you logged into your Galaxy instance UI using your admin account? This will display the Admin menu. Admin permissions are set up in the universe_wsgi.ini file: # -- Users and Security other items # Administrative users - set this to a comma-separated list of valid Galaxy # users (email addresses). These users will have access to the Admin section # of the server, and will have access to create users, groups, roles, # libraries, and more. For more information, see: # http://wiki.g2.bx.psu.edu/**Admin/Interfacehttp://wiki.g2.bx.psu.edu/Admin/Interface #admin_users = None Hopefully this solves the issue. Going forward, you'll probably find that the galaxy-...@bx.psu.edu mailing list is the most helpful for local install questions: http://wiki.g2.bx.psu.edu/**Support#Mailing_Listshttp://wiki.g2.bx.psu.edu/Support#Mailing_Lists Best, Jen Galaxy team On 5/8/12 2:10 PM, Tilahun Abebe wrote: Hi Galaxy users, I tried to install cutadapt for sequence trimming on a local Galaxy instance. I successfully installed Galaxy as an administrator. However, when Galaxy starts, I don't see the administrator option in the top menu bar with the Analyze Data, Workflow, Shared Data, Visualization, Help, and User. It looks like the only way I can install cutadapt is with an administrator option. Any suggestion how I can include the administrator option in the menu? Thanks for your help. Tilahun __**_ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/**listinfo/galaxy-devhttp://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson 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/
[galaxy-dev] Problem downloading results from MACS
Hi, I'm using Galaxy from the cloud (ID: pr...@ucdavis.edu) and I'm trying to download some .xls files (MACS' results that were successfully finished) and I'm obtaining the following error message: *Server Error** An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)* Please let me know how can I solve this problem. Thanks a lot, Yanina ___ 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] Loc file configuration question
Hi Raja, Can you check that your fields are tab separated and not spaces (they are spaces below, but that could be a copy and paste artifact)? Thanks for using Galaxy, Dan On May 9, 2012, at 9:45 AM, Raja Kelkar wrote: Hi Jen, Thank you for your response. I seem to have all the relevant entries in the two *.loc files you mentioned (paths in all_fasta files and the twobit files are different because of the way we have the files stored. I also converted the 2bit files to .fa and have them available in the same twobit directory). But the feature extraction is still not working. Here are the relevant entries in files (I have redacted specific file paths and replaced them with path_to): twobit.loc hg18/path_to/twobit/hg18.2bit hg19/path_to/twobit/hg19.2bit mm9/path_to/twobit/mm9.2bit mm8/path_to/twobit/mm8.2bit all_fasta.loc hg19fullhg19Human (Homo sapiens): hg19 Full /path_to/hg19/bwa_path/hg19_all.fa hg19_chr_only hg19_chrHuman (Homo sapiens): hg19_chrom_only /path_to/hg19/bwa_path/hg19.fa hg18fullhg18Human (Homo sapiens): hg18 Full /path_to/hg18/bwa_path/hg18_all.fa hg18_chr_only hg18_chrHuman (Homo sapiens): hg18_chrom_only /path_to/hg18/bwa_path/hg18_chrom_only.fa I assume that the second field in the (all_fasta.loc) file dbkey has to match the builds.txt file in the ucsc directory. Is that correct? It does in this case. I think I am missing something subtle here. The *.loc.sample files are great but the information contained in those is confusing. I am not sure why there are two examples of the same info (as far as I can tell) in most sample loc files. Thanks. On Tue, May 8, 2012 at 6:48 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Raja, This tool uses a database.2bit file to extract sequence data when the 'Locally cashed' option is used. The database is a genome that you install locally. .2bit format was developed by UCSC and they are the source for many genomes in this format already and for tools (compiled and uncompiled) to transform fasta data into/from .2bit format (faTwoToBit and twoBitToFa): http://hgdownload.cse.ucsc.edu/downloads.html (genomes + source) http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ (compiled utilities) For the extract tool, the builds list is required: http://wiki.g2.bx.psu.edu/Admin/Data%20Integration You don't actually need to have more NGS set up beyond that. Still, this wiki can help. http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup For example, the database.2bit file could be placed with your .fa files like: /galaxy-dist/tool-data/genome/databaseA/seq/databaseA.2bit /galaxy-dist/tool-data/genome/databaseA/seq/databaseA.fa /galaxy-dist/tool-data/genome/databaseB/bowtie/ /galaxy-dist/tool-data/genome/databaseB/sam/ /galaxy-dist/tool-data/genome/databaseB/seq/databaseB.2bit /galaxy-dist/tool-data/genome/databaseB/seq/databaseB.fa /galaxy-dist/tool-data/genome/databaseC/seq/databaseC.2bit /galaxy-dist/tool-data/genome/databaseC/seq/databaseC.fa /galaxy-dist/tool-data/genome/databaseD/seq/databaseD.2bit /galaxy-dist/tool-data/genome/databaseD/seq/databaseD.fa Then the .loc file is here: /galaxy-dist/tool-data/twobit.loc.sample You will probably have this for all genomes as well: /galaxy-dist/tool-data/all_fasta.loc.sample Remove the .sample before using these. Instructions for how to populate each are in the files themselves. The only gtf/gff files associated with this tool would be datasets from the history, so there are no gtf/gff data to stage before using the tool. To have the tool use a particular genome, set the query dataset (interval, bed, gtf) to have the same database identifier as you used for the database part of the database.2bit file. (This is why the builds list is required). If you make changes to data, don't forget to restart your server to see the changes. Hopefully this helps, Jen Galaxy team On 5/8/12 12:46 PM, Raja Kelkar wrote: I have two questions that pertain to a local install of galaxy: 1. I have been having trouble getting the “fetch sequences” à “extract genomic DNA” tool to work. Can someone identify the specific *.loc file that needs to have the info about the location of the genome sequence files? I get the following error when I run the extract tool: /No sequences are available for 'hg19’, request them by reporting this error./ // 2. What configuration file(s) need to contain locations for the gtf/gff files? Thanks. ___ 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/ -- Jennifer Jackson http://galaxyproject.org
[galaxy-dev] server error
Hi, I have run into a server error, how can I fix it? Thanks, Ashley ___ 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] Loc file configuration question
On 09/05/2012 22:40, Daniel Blankenberg wrote: Hi Raja, Can you check that your fields are tab separated and not spaces (they are spaces below, but that could be a copy and paste artifact)? Thanks for using Galaxy, Dan On May 9, 2012, at 9:45 AM, Raja Kelkar wrote: Hi Jen, Thank you for your response. I seem to have all the relevant entries in the two *.loc files you mentioned (paths in all_fasta files and the twobit files are different because of the way we have the files stored. I also converted the 2bit files to .fa and have them available in the same twobit directory). But the feature extraction is still not working. Here are the relevant entries in files (I have redacted specific file paths and replaced them with path_to): twobit.loc hg18 /path_to/twobit/hg18.2bit hg19 /path_to/twobit/hg19.2bit mm9 /path_to/twobit/mm9.2bit mm8 /path_to/twobit/mm8.2bit all_fasta.loc hg19full hg19 Human (Homo sapiens): hg19 Full /path_to/hg19/bwa_path/hg19_all.fa hg19_chr_only hg19_chr Human (Homo sapiens): hg19_chrom_only /path_to/hg19/bwa_path/hg19.fa hg18full hg18 Human (Homo sapiens): hg18 Full /path_to/hg18/bwa_path/hg18_all.fa hg18_chr_only hg18_chr Human (Homo sapiens): hg18_chrom_only /path_to/hg18/bwa_path/hg18_chrom_only.fa I assume that the second field in the (all_fasta.loc) file dbkey has to match the builds.txt file in the ucsc directory. Is that correct? It does in this case. I think I am missing something subtle here. The *.loc.sample files are great but the information contained in those is confusing. I am not sure why there are two examples of the same info (as far as I can tell) in most sample loc files. Thanks. On Tue, May 8, 2012 at 6:48 PM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hi Raja, This tool uses a database.2bit file to extract sequence data when the 'Locally cashed' option is used. The database is a genome that you install locally. .2bit format was developed by UCSC and they are the source for many genomes in this format already and for tools (compiled and uncompiled) to transform fasta data into/from .2bit format (faTwoToBit and twoBitToFa): http://hgdownload.cse.ucsc.__edu/downloads.html http://hgdownload.cse.ucsc.edu/downloads.html (genomes + source) http://hgdownload.cse.ucsc.__edu/admin/exe/linux.x86_64/ http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ (compiled utilities) For the extract tool, the builds list is required: http://wiki.g2.bx.psu.edu/__Admin/Data%20Integration http://wiki.g2.bx.psu.edu/Admin/Data%20Integration You don't actually need to have more NGS set up beyond that. Still, this wiki can help. http://wiki.g2.bx.psu.edu/__Admin/NGS%20Local%20Setup http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup For example, the database.2bit file could be placed with your .fa files like: /galaxy-dist/tool-data/genome/__databaseA/seq/databaseA.__2bit /galaxy-dist/tool-data/genome/__databaseA/seq/databaseA.fa /galaxy-dist/tool-data/genome/__databaseB/bowtie/ /galaxy-dist/tool-data/genome/__databaseB/sam/ /galaxy-dist/tool-data/genome/__databaseB/seq/databaseB.__2bit /galaxy-dist/tool-data/genome/__databaseB/seq/databaseB.fa /galaxy-dist/tool-data/genome/__databaseC/seq/databaseC.__2bit /galaxy-dist/tool-data/genome/__databaseC/seq/databaseC.fa /galaxy-dist/tool-data/genome/__databaseD/seq/databaseD.__2bit /galaxy-dist/tool-data/genome/__databaseD/seq/databaseD.fa Then the .loc file is here: /galaxy-dist/tool-data/twobit.__loc.sample You will probably have this for all genomes as well: /galaxy-dist/tool-data/all___fasta.loc.sample Remove the .sample before using these. Instructions for how to populate each are in the files themselves. The only gtf/gff files associated with this tool would be datasets from the history, so there are no gtf/gff data to stage before using the tool. To have the tool use a particular genome, set the query dataset (interval, bed, gtf) to have the same database identifier as you used for the database part of the database.2bit file. (This is why the builds list is required). If you make changes to data, don't forget to restart your server to see the changes. Hopefully this helps, Jen Galaxy team On 5/8/12 12:46 PM, Raja Kelkar wrote: I have two questions that pertain to a local install of galaxy: 1. I have been having trouble getting the “fetch sequences” à “extract genomic DNA” tool to work. Can someone identify the specific *.loc file that needs to have the info about the location of the genome sequence files? I get the following error when I run the extract tool: /No sequences are available for 'hg19’, request them by reporting this error./ // 2. What configuration file(s) need to
Re: [galaxy-dev] server error
Given the information supplied, I suggest a spatula. Many servers are quite adept with a spatula. Your results may vary. Bob H On May 9, 2012, at 4:43 PM, Ashley Tehranchi wrote: Hi, I have run into a server error, how can I fix it? Thanks, Ashley ___ 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] bowtie -X
Hello Jianpeng, The -X value of 1000 in Galaxy is more permissive than the Bowtie default value of 250. If you want to modify, then using a smaller test set of your specific data and working with the related parameters to see if the results are what you expect would be the best approach. Specifically - you'll probably want to look at what is kicked out as invalid if you lower the max threshold, and determine if that is good or bad for your experiment. Some more help is below (also on the tool form). You also asked me (direct): For local galaxy, can I update the tools freely ? For example, I want to update the Tophat. Will that work on our local galaxy if I update the Tophat ? If you are not intending to do tool development, then using the known dependencies is the recommendation. http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies That said, you are certainly free to modify any part of Galaxy that you want - tools, wrappers, and any other components are all options. Galaxy is open source. It is just important to know that changes in tools that deviate away from the known working version (and other dependencies) means that there are no guarantees about functionality. The tool wrapper and other tools that may interact with that tool (or actions, like workflows) could continue to be functional or be fully functional. Or, the tool could fail outright or have hidden bugs or other unpredictable problems with that tool itself or other Galaxy components it interacts with. These are not intractable problems - and this is exactly the process to upgrade a tool. To make the change then find the problems and fix them - and this is done all the time. I wanted to be clear about the scope because this is probably much more change than most want to deal with, unless development is the goal. Best, Jen Galaxy team --- The -X option is defined in the Bowtie manual at: http://bowtie-bio.sourceforge.net/manual.shtml#alignment It pairs with the -I option, both are here: -I/--minins int The minimum insert size for valid paired-end alignments. E.g. if -I 60 is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as -X is also satisfied). A 19-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -I constraint is applied with respect to the untrimmed mates. Default: 0. -X/--maxins int The maximum insert size for valid paired-end alignments. E.g. if -X 100 is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied). A 61-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -X constraint is applied with respect to the untrimmed mates, not the trimmed mates. Default: 250. These can interact with the -3 or -5 trimming options, in the manual: http://bowtie-bio.sourceforge.net/manual.shtml#input Also here: -5/--trim5 int Trim int bases from high-quality (left) end of each read before alignment (default: 0). -3/--trim3 int Trim int bases from low-quality (right) end of each read before alignment (default: 0). On 5/6/12 9:26 AM, Xu, Jianpeng wrote: Hi, I noticed that there is a parameter: Maximum insert size for valid paired-end alignments (-X) for bowtie on Galaxy. The default value on Galaxy is -X 1000. I was wondering if this is the default value we should use ? Or we need to change it to another value ? Thanks a lot. Jianpeng This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ 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/ -- Jennifer Jackson 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/
Re: [galaxy-dev] server error
I'm not sure what that means. From: Bob Harris rshar...@bx.psu.edu Date: Wednesday, May 9, 2012 1:49 PM To: Ashley Tehranchi a...@stanford.edu Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] server error Given the information supplied, I suggest a spatula. Many servers are quite adept with a spatula. Your results may vary. Bob H On May 9, 2012, at 4:43 PM, Ashley Tehranchi wrote: Hi, I have run into a server error, how can I fix it? Thanks, Ashley ___ 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] server error
Ashley: I think he was joking around. Essentially - to provide any help, people here need to know much more detail about what kind of server error occurred, and what input was provided so that the problem can be reproduced or a helpful suggestion can be made. This guide to asking good questions might be of some help to you: http://catb.org/~esr/faqs/smart-questions.html I probably can't help you with your actual problem, but if you can provide more information maybe somebody else can. some examples that might help. if you were running on the public galaxy server or not what you were trying to do what kind of data you where trying to analyze the contents of /var/log/galaxy/galaxy.log (or wherever the log is on your local installation) the results you see when you click on the bug icon in your failing history step Brad On May 9, 2012, at 6:51 PM, Ashley Tehranchi wrote: I'm not sure what that means. From: Bob Harris rshar...@bx.psu.edumailto:rshar...@bx.psu.edu Date: Wednesday, May 9, 2012 1:49 PM To: Ashley Tehranchi a...@stanford.edumailto:a...@stanford.edu Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] server error Given the information supplied, I suggest a spatula. Many servers are quite adept with a spatula. Your results may vary. Bob H On May 9, 2012, at 4:43 PM, Ashley Tehranchi wrote: Hi, I have run into a server error, how can I fix it? Thanks, Ashley ___ 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/ -- Brad Langhorst langho...@neb.commailto:langho...@neb.com 978-380-7564 ___ 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] Galaxy Tool Shed upload error
Hi Galaxy team, I am trying to upload a tool wrapper to main tool shed http://toolshed.g2.bx.psu.edu and ending up with a 'server error' message. Could you please let me know what is going wrong here. thanks, --Vipin ___ 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] Server Error when downloading files from history
Hi there, I received the following error when trying to download/save my tabular files with 5k lines: Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Please help! Thanks in advance. Cheers, Rathi -- Rathi D. Thiagarajan, PhD Professional Scientific Collaborator UCSD Research Scholar Dept. of Chemical Physiology Center for Regenerative Medicine The Scripps Research Institute 3030 Science Park Rd, La Jolla, CA 92035, USA Mail:SP30-3021 W: 858.784.7753 E: ra...@scripps.edu E: rthiagara...@ucsd.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] Galaxy Tool Shed upload error
Hi Vipin, I believe I've fixed the problem that you encountered - the tool shed has been updated with the fix. Thanks for reporting this! If you see additional problems, please let me know - I assume I discovered the correct exception in the log. Thanks! Greg Von Kuster On May 9, 2012, at 7:44 PM, Vipin TS wrote: Hi Galaxy team, I am trying to upload a tool wrapper to main tool shed http://toolshed.g2.bx.psu.edu and ending up with a 'server error' message. Could you please let me know what is going wrong here. thanks, --Vipin ___ 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] Interested in speaking with other institutions deploying Galaxy locally?
Hi all, I'm at one of the places Ross mentions (VLSCI), with Enis - among other things we're deploying Galaxy CloudMan on the new Australian Research Cloud. Just from talking to people I feel that local institutions that have installed their own Galaxy, and are customising it, wrapping tools for the researchers they support etc, do end up struggling with a lot of the same problems. I think though that as Ross is suggesting in a lot of cases these needs could be filled by the existing galaxy-user and galaxy-dev mailing lists (I find sometimes people can be quite hesitant to post a question until they have spent a lot of time on the problem). I do like the idea of a local Australia-New Zealand Galaxy group for developers / techie bioinformaticians, but more for the sake of face-to-face interaction and perhaps local-timezone teleconferences; I don't want to end up just duplicating existing mailing lists. I'm not sure of the best way to make such a group take off or how much interest there would be. If there are other Australian / New Zealand or local timezone groups reading this list and you're interested, let us know! Clare On 30 April 2012 13:35, Ross ross.laza...@gmail.com wrote: To all interested in Dave's suggestion: IMHO, an Australian/New Zealand Galaxy user/deployer/developer group will be worth setting up and will be viable if it solves specific problems that aren't adequately addressed by existing networks and communication channels - otherwise it will be JAFUG (just another fleeting user group) and will likely fizzle due to lack of genuine utility to potential participants. EG: One challenge for us when it comes to (eg) the proposed teleconferences is the tyranny of time zones - being 14 hours ahead of EST eg in Melbourne/Sydney. The other big challenge is that travel to meetings in Europe or the USA is expensive and exhausting, so workshops and hands on training are harder to get to. In general, I think we're probably going to be able to find plenty of problems to do with geographic isolation and maybe even some specific Australian challenges - but let's be clear about exactly what those are before we start building any structures. One problem I keep seeing is that there are many organisations happy to invest in hardware infrastructure, but far less willing to invest in the training and staff development needed for success. Two things I'd like to suggest to help with planning: 1) to get a better idea of scope, it would be very handy to assemble a register of potential organisations and their primary contacts. I already know of some large Australian organisations investing heavily in Galaxy deployment - eg - VLSCI in Melbourne; UQ in Brisbane, CSIRO all over the place, the Victorian DPI, AGRF, and the BakerIDI where I'm based - no doubt there are plenty of others too? 2) to make sure the idea is viable, it would be useful to collect some specific deployment challenges that people are experiencing that some kind of local user's group could help overcome? One focus I have a personal interest in exploring would be in face to face educational activities: eg for local Galaxy instance system administrators? Local tool developers? Local biologist users in specific contexts like short read sequencing? Suggestions welcomed... On Mon, Apr 30, 2012 at 12:37 PM, Dave Clements cleme...@galaxyproject.org wrote: Hi Ryan, Ann, and everyone else I second what Nate says (I always do :-). I too like that it is user driven. And, while I am not a developer, I do plan on being on the call as often as possible. I can also offer my support for logistical and any other support. Ann, please let me know if you want help with getting this going and getting the word out. On a related note, With Matloob's email, we have at least 3 organizations in Australia and New Zealand that are interested. I know that there are many more Galaxy installations in that part of the world (and you have Enis and Ross in Australia now). Would this be a good opportunity to set up the first (to my knowledge) regional user group? If anyone thinks this is a good idea, please respond (and create a new thread). Finally, Ann, thanks for starting this. Dave C I also that both Ross and Enis are in Australia now On Sun, Apr 29, 2012 at 10:24 AM, Nate Coraor n...@bx.psu.edu wrote: Hi Ryan, I like that it's user-directed, and we could be there to provide input, although if help is needed to organize the call we could probably assist with that. I plan to be on the call as often as my schedule allows, and I believe some of the other developers on the team would also be interested. --nate On Apr 28, 2012, at 8:49 AM, Ryan Golhar wrote: One question - Are the Galaxy developers involved in this or is this for user's only? It may be helpful to have developers on the call to provide information that users do not necessarily have.
