galaxy-dev November 2013

galaxy-dev@lists.galaxyproject.org

83 participants
135 discussions

unable to share dataset history
by Manisha Sapre 20 Nov '13

20 Nov '13

Hello Team Galaxy trying to share/ forward dataset history from user 1 ( running on a local instance,Scrn.1) to user 2 (running on cloud amazon ec2 instance,Scrn.2) and vice-versa, error:- user is not a valid galaxy user. getting this error while both the users are logged into system and both the instance's are running normal. insights of team will be very helpful. Thanks msapre [cid:EE64498E-7E1E-49C1-BD89-8AAB2EA54F11] [cid:8CB45B82-801C-4016-A17A-9FE4ED7F8C2E]

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Re: [galaxy-dev] secure Galaxy with SSL
by Jingchao Zhang 19 Nov '13

19 Nov '13

Hi Peter, Thanks so much for your help! It is like you said a browser issue. I also noticed that the Galaxy main server (https://usegalaxy.org/) doesn't have this problem. And their USCS main table browser uses "https" instead of "http". Does anyone know why this isn't included in the current Galaxy release? And how can I change my current "http USCS main" to "https USCS main"? Thanks, Jim Message: 8 Date: Tue, 19 Nov 2013 08:51:03 +0000 From: Peter Briggs <peter.briggs(a)manchester.ac.uk> To: galaxy-dev(a)lists.bx.psu.edu Subject: Re: [galaxy-dev] secure Galaxy with SSL Message-ID: <528B2677.9050706(a)manchester.ac.uk> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hello Jim Re your problem #1 (UCSC browser appears to be blocked), I've seen something similar with our local Galaxy instance, which is also served via https. In our case I believe this is actually a browser issue: the latest version of Firefox silently blocks mixed secure and insecure content: https://blog.mozilla.org/tanvi/2013/04/10/mixed-content-blocking-enabled-in… (I think Chrome and IE do something similar, although IE at least gives a warning.) The workaround is either to disable mixed content blocking (not trivial in Firefox, and probably not a good idea in general), or to do something like e.g. right-click "Open link in new tab" on the "Get data"/"UCSC main table browser" link in Galaxy. Once UCSC has loaded in the new tab it can be used to send data back to Galaxy without any problems. HTH Best wishes, Peter On 18/11/13 23:03, Jingchao Zhang wrote: > Dear all, > > Today I installed the SSL module for our local Galaxy instance and the > "https://" link is working fine. I added this > "<Location"/"> > > RequestHeader set X-URL-SCHEME https > > </Location>" > in our Apache configuration file as instructed in this webpage: > http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy > > Here are my problems with SSL: > 1. Some build in links like "UCSC Main > <http://genome.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=https%3A//hcc-galaxy.unl…> table > browser" and "UCSC Test > <http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=https%3A//hcc-g…> table > browser" become invalid. If I click on them, nothing will happen, as if > they are blocked. > 2. The old "http" link still works, which I think shouldn't because I > added the "RequestHeader ... https" line in Apache configuration. I > really want to disable the http link because the new users could be > easily led to the old one. > > Both httpd and Galaxy have been restarted after the changes are made. > Since I didn't find any similar threads in the mailist, I hope someone > here can help me out with this. > > Thanks, > Jim > > > ___________________________________________________________ > 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/ > -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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wigTobigwig error: broken pipe and len file not found
by ruiwang.sz 19 Nov '13

19 Nov '13

Hi All, I‘m seeing some weird error messages...I googled but didn't see anything useful: So, it is during the wigToBigwig conversion: Dataset generation errors Dataset 47: Wig/BedGraph-to-bigWig on data 43 Tool execution generated the following error message: grep: writing output: Broken pipe grep: writing output: Broken pipe grep: writing output: Broken pipe and many more lines of the same error The tool produced the following additional output: Couldn't open tool-data/shared/ucsc/chrom/mm10.len , No such file or directory but it is there: ls -l tool-data/shared/ucsc/chrom/mm10.len -rw-rw-r-- 1 bioinfoadmin bioinfoadmin 1405 Oct 9 11:33 tool-data/shared/ucsc/chrom/mm10.len >From the Galaxy server log, I found these: galaxy.tools WARNING 2013-11-15 17:46:43,200 Failed to resolve dependency on 'ucsc_tools', ignoring galaxy.jobs.runners.local DEBUG 2013-11-15 17:46:43,255 (216) executing: grep -v "^track" /home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_458.dat | wigToBigWig stdin tool-data/shared/ucsc/chrom/mm10.len /home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_473.dat -blockSize=256 -itemsPerSlot=1024 -clip 2>&1 || echo "Error running wigToBigWig." >&2 and then, setmetadata set the dataset state to ERROR. I did verify that the result dataset_473.dat has a size 0. However, when I run the command alone: grep -v "^track" /home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_458.dat | wigToBigWig stdin tool-data/shared/ucsc/chrom/mm10.len /home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_473.dat -blockSize=256 -itemsPerSlot=1024 -clip it successfully generated the dataset_473.dat. also, I look into the wig_to_Bigwig.xml in tools/filters, the command is: grep -v "^track" $input1 | wigToBigWig stdin $chromInfo $out_file1 however, I don't see where this "$chromInfo" was defined, yet it indeed found the the correct value: tool-data/shared/ucsc/chrom/mm10.len. how does that happen? it is very puzzling...I'm not sure if anyone has seen this before, please let me know! Thanks, Rui

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Next GalaxyAdmins Meetup: November 20
by Dave Clements 19 Nov '13

19 Nov '13

Hello all, The next GalaxyAdmins meetup will be Wednesday, November 20, at 10am US Central time. See the meetup page<http://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2013_11_20> for a link and directions for connecting to the meetup. *GCC2013 GalaxyAdmins BoF Followup* This is our first meetup since the GCC2013 GalaxyAdmins BoF<http://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyAdmins> where we discussed what the group should focus on going forward, and what the Galaxy Project can do to support the group. As suggested at GCC2013, followup to that discussion will be the main topic for this meetup. We came out with several action items and one piece of unfinished business (leadership). Also, as suggested at the GCC2013 BoF, we would like to encourage discussion in the week before the meetup. Therefore, 1. Please review the notes from the GCC2013 GalaxyAdmins BoF<http://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyAdmins> 2. Take a look at these two draft implementations of action items from that discussion: 1. Galaxy Deployment Pages<http://wiki.galaxyproject.org/Community/Deployments> 2. Galaxy Log Pages <http://wiki.galaxyproject.org/Community/Logs> And, if you see anything that you want to comment on please reply to this thread on the Galaxy-Dev list. I'll update other actions as the call gets closer. *Galaxy Project Update: Main moves to TACC* Nate Coraor will give the project update, focusing on the recent move of UseGalaxy.org to TACC. We hope to see (well, hear) you there, and please don't hesitate to ask if you have any questions. Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Empty tool panel
by Yec'han Laizet 19 Nov '13

19 Nov '13

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 ================================================

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secure Galaxy with SSL
by Jingchao Zhang 19 Nov '13

19 Nov '13

Dear all, Today I installed the SSL module for our local Galaxy instance and the "https://" link is working fine. I added this "<Location "/"> RequestHeader set X-URL-SCHEME https </Location>" in our Apache configuration file as instructed in this webpage: http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy Here are my problems with SSL: 1. Some build in links like "UCSC Main<http://genome.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=https%3A//hcc-galaxy.unl…> table browser" and "UCSC Test<http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=https%3A//hcc-g…> table browser" become invalid. If I click on them, nothing will happen, as if they are blocked. 2. The old "http" link still works, which I think shouldn't because I added the "RequestHeader ... https" line in Apache configuration. I really want to disable the http link because the new users could be easily led to the old one. Both httpd and Galaxy have been restarted after the changes are made. Since I didn't find any similar threads in the mailist, I hope someone here can help me out with this. Thanks, Jim

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ACTION needed: fix error in Cloud Cluster Galaxy Trackster DATE needed: needed for workshop on Wednesday 20 November
by Young, Lynn (NIH/OD/ORS) [E] 18 Nov '13

18 Nov '13

Hi, We're using Galaxy Cloud -> New Cloud Cluster to create instances of Galaxy for training on Wednesday 20 November. When we try to view a bam file using Trackster, we get the following error: /opt/sge/default/spool/execd/ip-10-32-111-66/job_scripts/14: line 13: bedtools: command not found /opt/sge/default/spool/execd/ip-10-32-111-66/job_scripts/14: line 13: bedGraphToBigWig: command not found Please let us know how to proceed. Sincerely, Lynn Lynn Young, PhD | Informationist/Bioinformatics Scientist | National Institutes of Health Library | Office of Research Services | Building 10, Room B1L-306D | 10 Center Drive | Bethesda, Maryland 20892-1150 | T. 301-594-6426 | F. 301-402-0254 | E. lynny(a)mail.nih.gov<mailto:lynny@mail.nih.gov> | http://twitter.com/bioinformatics1 Stay connected with the NIH Library NIH Library: http://nihlibrary.nih.gov<http://nihlibrary.nih.gov/> | Facebook: http://www.facebook.com/nihlibrary | Twitter: http://www.twitter.com/nihlib<http://www.twitter.com/nihlib> _____________________________ Amazing Research. Amazing Help.

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BAM/BAI index file test problem on (Test) Tool Shed
by Peter Cock 18 Nov '13

18 Nov '13

Hi guys, I have a new wrapper for samtools idxstats with a working unit test via run_functional_tests.sh run locally or on TravisCI: https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-November/017406.html However, this tool's test is failing on the Test Tool Shed: http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats/6564815949… Tool test results Automated test environment Time tested: ~ 11 hours ago System: Linux 3.8.0-30-generic Architecture: x86_64 Python version: 2.7.4 Galaxy revision: 11284:28469a503b56 Galaxy database version: 117 Tool shed revision: Tool shed database version: Tool shed mercurial version: Tests that failed Tool id: samtools_idxstats Tool version: samtools_idxstats Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterj…) Stderr: Fatal error: Exit code 1 () Input BAI file not found: None Traceback: Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 216, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 28, in do_it self.__verify_outputs( testdef, shed_tool_id, data_list ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 134, in __verify_outputs self.__verify_output( output_tuple, shed_tool_id, elem, maxseconds=maxseconds ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 141, in __verify_output self.verify_dataset_correctness( outfile, hid=elem_hid, attributes=attributes, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 782, in verify_dataset_correctness self._assert_dataset_state( elem, 'ok' ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 606, in _assert_dataset_state raise AssertionError( errmsg ) AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error It appears that the upload has not generated the *.bai index and assigned it to the variable input_bam.metadata.bam_index (but this works via run_functional_tests.sh for me): $ ls test-data/ex1.* test-data/ex1.bam test-data/ex1.idxstats.tabular $ ./run_functional_tests.sh -id samtools_idxstats ... Ran 1 test in 32.400s OK ... (all fine) (Note that the bai file does not seem to be needed) Tested with this revision, which works: $ hg branch default $ hg log | head changeset: 12309:1df960b4892a tag: tip user: John Chilton <jmchilton(a)gmail.com> date: Sun Nov 10 23:37:56 2013 -0600 summary: PEP-8 cleanups of lib/galaxy/security/__init__.py. Updated to current tip, also works: $ hg branch default [galaxy@ppserver galaxy-central]$ hg log | head changeset: 12321:e12a10e5418d tag: tip user: guerler date: Mon Nov 11 16:00:10 2013 -0500 summary: UI: Fix tooltip placement for masthead icons Are there anyone known differences on the Test Tool Shed which could explain this failure? Thanks, Peter

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Tool unit tests using composite datatypes
by Peter Cock 18 Nov '13

18 Nov '13

Hello all, I'd like to be able to write some simple <test> entries for some of the BLAST+ tools using composite datatypes as input or output (i.e. small BLAST databases). This doesn't seem to be mentioned or hinted at on the wiki: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax?action=show&redi… Is it possible to use a composite datatype as a test input? If so how? Normal datatypes are loaded into the test history using using the upload tool - does that mean I first need to extend the relevant datatypes to allow them to be uploaded? Example: Run blastp using a small query FASTA file and a small database, check the output (eg tabular). Is it possible to use a composite datatype as a test output? If so how? Example: Run makeblastdb using a small FASTA file, and check the output (a small BLAST database). Thanks, Peter

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tardis job splitter
by McCulloch, Alan 18 Nov '13

18 Nov '13

dear all, There have been a few posts lately about doing distributed computing via Galaxy - i.e. job splitters etc - below a contribution of some ideas we have developed and applied in our work, where we have arranged for some Galaxy tools to execute in parallel on our cluster. We have developed a job-splitter script "tardis.py" (available from https://bitbucket.org/agr-bifo/tardis), which takes marked-up standard unix commands that run an application or tool. The mark-up is prefixed to the input and output command-line options. Tardis strips off the mark-up, and re-writes the commands to refer to split inputs and outputs, which are then executed in parallel e.g. on a distributed compute resource. Tardis knows the output files to expect and how to join them back together. (This was referred to in our GCC2013 talk http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Events.2FGCC2013.2FA… ) Any reasonable unix based data processing or analysis command may be marked up and run using tardis, though of course tardis needs to know how to split and join the data. Our approach also assumes a "symmetrical" HPC cluster configuration, in the sense that each node sees the same view of the file system (and has the required underlying application installed). We use tardis to support both Galaxy and command-line based compute. Background / design pattern / motivating analogy: Galaxy provides a high level "end to end" view of a workflow; the HPC cluster resource that one uses then involves spraying chunks of data out into parallel processes, usually in the form of some kind of distributed compute cluster - but an end-user looking at a Galaxy history, should ideally not be able to tell whether the workflow was run as a single process on the server, or via many parallel processes on the cluster (apart from the fact that when run in parallel on the cluster, its alot faster!). We noticed that the TCP / IP layered networking protocol stack provides a useful metaphor and design pattern - with the "end to end" topology of a Galaxy workflow corresponding to the transport layer of TCP/ IP; and the distribution of computation across a cluster corresponding to the next TCP/IP layer down - the packet-routing layer. This picture suggested a strongly layered approach to provisioning Galaxy with parallelised compute on split data, and hence to an approach in which the footprint in the Galaxy code-base, of parallel / distributed compute support, should ideally (from the layered-design point of view) be minimal and superficial. Thus in our approach so far, the only footprint is in the tool config files, where we arrange the templating to (optionally) prefix the required tardis mark-up to the input and output command options, and the tardis script name to the command as a whole. tardis then takes care of rewriting and launching all of the jobs, and finally joining the results back together and putting them where galaxy expects them to be (and also housekeeping such as collating and passing up stderr and stdout , and appropriate process exit codes). (For each galaxy job, tardis creates a working folder in a designated scratch area, where input files are uncompressed and split; job files and their output are stored; logging is done etc. Split data is cleaned up at the end unless there was an error in some part of the job, in which case everything is retained for debugging and in some cases restart) (We modify Galaxy tool-configs so that the user can optionally choose to run the tool on our HPC cluster - there are three HPC related input fields, appended to the input section of a tool. Here the user selects whether they want to use our cluster and if so, they specify the chunk size, and can also at that point specify a sampling rate, since we often find it useful to be able to run preliminary analyses on a random sample of (for example) single or paired-end NGS sequence data, to obtain a fairly quick snapshot of the data, before the expense of a complete run. We found it convenient to include support for input sampling in tardis). The pdf document at https://bitbucket.org/agr-bifo/tardis includes a number of examples of marking up a command, and also a simple example of a galaxy tool-config that has been modified to include support for optionally running the job on our HPC cluster via the tardis pre-processor. Known limitations: * we have not yet attempted to integrate our approach with the existing Galaxy job-splitting distributed compute support, partly because of our "layered" design goal (admittedly also partly because of ignorance about its details ! ) * our current implementation is quite naive in the distributed compute API it uses - it supports launching condor job files (and also native sub-processes) - our plan is to replace that with using the drmaa API * we would like to integrate it better with the galaxy type system, probably via a galaxy-tardis wrapper We would be keen to contribute our approach to Galaxy if people are interested. Cheers Alan McCulloch Bioinformatics Software Engineer AgResearch NZ

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galaxy-dev November 2013