galaxy-dev June 2016

galaxy-dev@lists.galaxyproject.org

49 participants
54 discussions

Re: [galaxy-dev] cleanup datasets error
by Rathert, Philipp, Dr. 14 Jun '16

14 Jun '16

Hi Bjoern, I edited the galaxy.ini directly and started the script. Unfortunately I get a different error: Traceback (most recent call last): File "scripts/cleanup_datasets/cleanup_datasets.py", line 544, in <module> main() File "scripts/cleanup_datasets/cleanup_datasets.py", line 104, in main app = CleanupDatasetsApplication( config ) File "scripts/cleanup_datasets/cleanup_datasets.py", line 529, in __init__ self.model = galaxy.model.mapping.init( config.file_path, config.database_connection, engine_options={}, create_tables=False, object_store=self.object_store ) File "/galaxy-central/lib/galaxy/model/mapping.py", line 2541, in init engine = build_engine( url, engine_options, database_query_profiling_proxy, trace_logger ) File "/galaxy-central/lib/galaxy/model/orm/engine_factory.py", line 20, in build_engine engine = create_engine( url, proxy=proxy, **engine_options ) File "/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/__init__.py", line 386, in create_engine return strategy.create(*args, **kwargs) File "/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 75, in create dbapi = dialect_cls.dbapi(**dbapi_args) File "/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py", line 579, in dbapi import psycopg2 ImportError: No module named psycopg2 Can I install the python-psycopq2 module via apt-get in the container and would this help to fix thee issue? Cheers, Philipp -----Original message----- From: Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de> Sent: Tuesday 14th June 2016 9:56 To: Bjoern Gruening <bjoern.gruening(a)gmail.com> Cc: galaxy-dev <galaxy-dev(a)lists.galaxyproject.org> Subject: Re: [galaxy-dev] cleanup datasets error Hi Bjoern, This is wired. It worked before... I will add this to the galaxy.ini in the config folder and try again. Cheers, Philipp ---Philipp on the road--- Am 14.06.2016 um 09:50 schrieb Bjoern Gruening <bjoern.gruening(a)gmail.com <mailto:bjoern.gruening@gmail.com> >: Hi, I don't think this will work with the script. This script reads the config file you specify config/galaxy.ini. And hence it needs to be added in this file, not via -e variables. This is probably something we should improve. Ciao, Bjoern > cleanup datasets error > > HI Björn, > > > > I have added these to the galaxy.ini via the docker specific e- > variables during startup of the container. > > > > How can I check if they are broken? > > > > Cheers, > > > > Philipp > > > > *From:*Bjoern Gruening [mailto:bjoern.gruening@gmail.com] *Sent:* > Tuesday, June 14, 2016 9:30 AM *To:* Rathert, Philipp, Dr. > <philipp.rathert(a)ibc.uni-stuttgart.de>; galaxy-dev > <galaxy-dev(a)lists.galaxyproject.org> *Subject:* Re: [galaxy-dev] > cleanup datasets error > > > > Hi Philipp, > > have you followed this from the readme? > > > Note that if you would like to run any of the cleanup scripts ><https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%2…>, > you will need to add the following to > |/export/galaxy-central/config/galaxy.ini|: > > |database_connection = > postgresql://galaxy:galaxy@localhost:5432/galaxy| |file_path = > /export/galaxy-central/database/files| > > Or is this broken? Cheers, Bjoern > > On 14.06.2016 09:21, Rathert, Philipp, Dr. wrote: > > Dear all, > > > > when I want to start the cleanup datasets script I get the following > error. > > > > (.venv)root@galaxy:/galaxy-central# python > /galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py > config/galaxy.ini -d -10 -1 > > Traceback (most recent call last): > > File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", > line 544, in <module> > > main() > > File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", > line 99, in main > > for key, value in config_parser.items( "app:main" ): > > File "/usr/lib/python2.7/ConfigParser.py", line 642, in items > > raise NoSectionError(section) > > ConfigParser.NoSectionError: No section: 'app:main' > > > > > > We are using the docker galaxy stable 16.04 version. Before this > script always worked without producing any error. > > > > It would be great if anybody has an idea how to fix this... > > > > Thank you very much in advance. > > > > Cheers, > > > > Philipp > > > > > > -----Original message----- *From:* Marius van den Beek > <m.vandenbeek(a)gmail.com> <mailto:m.vandenbeek@gmail.com> *Sent:* > Tuesday 7th June 2016 14:06 *To:* Marco Tangaro > <ma.tangaro(a)gmail.com> <mailto:ma.tangaro@gmail.com> *Cc:* galaxy-dev > <galaxy-dev(a)lists.galaxyproject.org> > <mailto:galaxy-dev@lists.galaxyproject.org> *Subject:* Re: > [galaxy-dev] Python tool wrapper with multiple input and output > files > > > Hi Marco, > > > > you've got an interesting use-case there. > > You may want to use either a dataset list (if you only supply > rna_n.bam), > > or a paired dataset list (rna_n.bam and dna_n.bam). > > I would probably implement a conditional, where the user selects > either a dataset list or a paired dataset list. > > The output would then be another collection of output files. > > Have a look at the test tool folder, and see if any of the tools > named collection_*.xml fits what you would like to do > > https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools > > > These two may be a good basis for what you want to achieve: > >https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/coll… > > > [this one creates an output collection] > >https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/coll… > > > [this one has a conditional to either select a list or a paired list as input] > > > > Let us know if you need more help! > > > > Cheers, > > Marius > > > > On 7 June 2016 at 09:50, Marco Tangaro <ma.tangaro(a)gmail.com > <mailto:ma.tangaro@gmail.com>> wrote: > > Dear experts, my name is Marco and I'm working to port our python > tool to the Galaxy framework. The main script needs a rna.bam file as > input, a reference fasta file, both mandatory. Finally, you can add a > dna.bam file, but this is optional. Therefore an example command is: > > script.py -i rna.bam -f reference.fa -j dna.bam > > The outout is a tabular. Again the -j dna.bam option is completely > optional. So quite soon it turned out that I had to use a python > wrapper to parse our script. Now the wrapper works fine. > > > The next step is to run the tool over multiple input file and we > would like to avoid to use a workflow. > > The idea is that to each input file corresponds an output file. The > reference is still the same. For instance, we have: > > rna_1.bam + dna_1.bam -> output_1.txt rna_2.bam + dna_2.bam -> > output_2.txt rna_3.bam + dna_3.bam -> output_3.txt ... and so on. > > > But I don't know the best strategy to give to my wrapper multiple > input files. Moreover I have to be sure, when the dna_xyz.bam files > are uploaded, that they correspond to the right rna_xyz.bam file. > > I would like to have as output a page which is showing as results the > link to the single output files as suggested here. > https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files > planning to integrate a javascript interface. > > I've browsed a lot, but on multiple input file the posts are old. I'm > using the last galaxy release (16_04). > > I'm quite new to the galaxy world... Thanks a lot for your > suggestions, Marco > > > ___________________________________________________________ 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: https://lists.galaxyproject.org/ > > 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: > > https://lists.galaxyproject.org/ > > > > 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

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cleanup datasets error
by Rathert, Philipp, Dr. 14 Jun '16

14 Jun '16

Dear all, when I want to start the cleanup datasets script I get the following error. (.venv)root@galaxy:/galaxy-central# python /galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d -10 -1 Traceback (most recent call last): File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", line 544, in <module> main() File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", line 99, in main for key, value in config_parser.items( "app:main" ): File "/usr/lib/python2.7/ConfigParser.py", line 642, in items raise NoSectionError(section) ConfigParser.NoSectionError: No section: 'app:main' We are using the docker galaxy stable 16.04 version. Before this script always worked without producing any error. It would be great if anybody has an idea how to fix this... Thank you very much in advance. Cheers, Philipp -----Original message----- From: Marius van den Beek <m.vandenbeek(a)gmail.com> Sent: Tuesday 7th June 2016 14:06 To: Marco Tangaro <ma.tangaro(a)gmail.com> Cc: galaxy-dev <galaxy-dev(a)lists.galaxyproject.org> Subject: Re: [galaxy-dev] Python tool wrapper with multiple input and outputfiles Hi Marco, you've got an interesting use-case there. You may want to use either a dataset list (if you only supply rna_n.bam), or a paired dataset list (rna_n.bam and dna_n.bam). I would probably implement a conditional, where the user selects either a dataset list or a paired dataset list. The output would then be another collection of output files. Have a look at the test tool folder, and see if any of the tools named collection_*.xml fits what you would like to do https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools These two may be a good basis for what you want to achieve: https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/coll… [this one creates an output collection] https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/coll… [this one has a conditional to either select a list or a paired list as input] Let us know if you need more help! Cheers, Marius On 7 June 2016 at 09:50, Marco Tangaro <ma.tangaro(a)gmail.com <mailto:ma.tangaro@gmail.com> > wrote: Dear experts, my name is Marco and I'm working to port our python tool to the Galaxy framework. The main script needs a rna.bam file as input, a reference fasta file, both mandatory. Finally, you can add a dna.bam file, but this is optional. Therefore an example command is: script.py -i rna.bam -f reference.fa -j dna.bam The outout is a tabular. Again the -j dna.bam option is completely optional. So quite soon it turned out that I had to use a python wrapper to parse our script. Now the wrapper works fine. The next step is to run the tool over multiple input file and we would like to avoid to use a workflow. The idea is that to each input file corresponds an output file. The reference is still the same. For instance, we have: rna_1.bam + dna_1.bam -> output_1.txt rna_2.bam + dna_2.bam -> output_2.txt rna_3.bam + dna_3.bam -> output_3.txt ... and so on. But I don't know the best strategy to give to my wrapper multiple input files. Moreover I have to be sure, when the dna_xyz.bam files are uploaded, that they correspond to the right rna_xyz.bam file. I would like to have as output a page which is showing as results the link to the single output files as suggested here. https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files planning to integrate a javascript interface. I've browsed a lot, but on multiple input file the posts are old. I'm using the last galaxy release (16_04). I'm quite new to the galaxy world... Thanks a lot for your suggestions, Marco ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>

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how to get raw input from GUI
by Beginner TI 13 Jun '16

13 Jun '16

Hi, I am working on a wrapper for gatk and including <repeat name="filters" title="filter names and expressions" help="--filterName, --filterExpression"> <param name="filter_name" type="text" value="" title="Filter name to be included in the analysis" /> <param name="filter_exp" type="data" value="" title="Filter expression to be included in the analysis" /> </repeat> in it, however, when I reference it using ${filter.filter_exp} it would translate 'FS > 30.0' into XXXFS __gt__ 30.0XXX is there a way that I could keep the original text string 'FS > 30.0'? I did a quick lookup online but didn't see anything in cheetah's user guide or other places. Thanks, Rui

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Re: [galaxy-dev] Deploying custom genome in Galaxy for use with ANNOVAR (Peter Briggs)
by David Kovalic 13 Jun '16

13 Jun '16

Peter, Thanks! The blog post is very helpful. David > ---------- Forwarded message ---------- > From: Peter Briggs <peter.briggs(a)manchester.ac.uk> > To: galaxy-dev(a)lists.galaxyproject.org > Cc: > Date: Wed, 8 Jun 2016 08:25:03 +0100 > Subject: Re: [galaxy-dev] Deploying custom genome in Galaxy for use with > ANNOVAR > Hello David > > I don't think it will answer all your questions, however: I wrote up my > experiences with installing ANNOVAR in Galaxy last year which might be > useful as a starting point: > > > http://galacticengineer.blogspot.co.uk/2015/03/installing-annovar-in-galaxy… > > As I recall all the databases we installed were standard ones from > ANNOVAR. However the above instructions might be useful in at least > getting started. > > Apologies if I've misunderstood your question and this doesn't help, > > Best wishes > > Peter > > On 07/06/16 17:48, David Kovalic wrote: > > All, > > > > From my read of the command line docs for ANNOVAR I believe that the > > program needs so ancillary files for its operation (e.g. GenePred file, > > transcripts fasta file, etc...). > > > > Does anyone have any experience deploying custom genomes in Galaxy for > > use with ANNOVAR? Specifically what files need to go where in order to > > enable the Galaxy ANNOVAR front end? > > > > Thanks, > > > > David > > > > > > ___________________________________________________________ > > 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: > > https://lists.galaxyproject.org/ > > > > 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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Compiler & OS questionnaire
by Björn Grüning 13 Jun '16

13 Jun '16

Hi, the conda community is currently doing a survey on the buildchain requirements of the scientific community and want to know if we need binaries that run under old systems like CentOS-5 or if CentOS-6 and newer is sufficient. Galaxy supports conda since a few releases and we have plans to advertise this dependency resolver more and more in the near future. It would be great to know how many of you run Galaxy on an old system like CentOS-5 or if it would be ok if it would be ok to only support systems newer than CentOS-6. Please fill out this survey: https://t.co/q0l2mkS5Na Thanks a lot! Bjoern

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Trinity installation
by Jose Juan Almagro Armenteros 10 Jun '16

10 Jun '16

Hello, I am having troubles installing the last version of the tool Trinity. I found that I have the same error as this issue ( https://github.com/galaxyproject/galaxy/issues/1947), so I tried the suggested solution. It didn't work, so I posted the error in the issue. Then, I tried to change the tmp folder to another one in the same filesytem (and undoing the previous solution). Again it didn't work, but it gave a different error: File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 123, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( install_environment, tool_dependency, actions_dict ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 108, in install_and_build_package initial_download=False ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 31, in execute_step initial_download=initial_download ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 845, in execute_step destination_dir=os.path.join( action_dict[ 'destination_directory' ] ) ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 864, in move_directory_files shutil.move( source_file, destination_file ) File "/usr/lib/python2.7/shutil.py", line 130, in copy2 copyfile(src, dst) File "/usr/lib/python2.7/shutil.py", line 82, in copyfile with open(src, 'rb') as fsrc: [Errno 21] Is a directory: '/steno-internal/projects/galaxy/galaxy-dist/tmp/tmp-toolshed-mtd8Exq2w/trinityrnaseq-2.1.1/trinity-plugins/jellyfish' I am using the Galaxy release *16.01. *Do you know how could I solve this problem?

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Using session parameters in Galaxy tools
by Amelia Ireland 09 Jun '16

09 Jun '16

Is it possible to access session parameters and use them in Galaxy tool wrappers? If so, how? I am integrating Galaxy with a local system, and I need the current session ID to be able to access user and session-specific data. I am already getting the user email as $__user_email__ (from https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccommand.3E_… ). Any suggestions gratefully received. Thanks!

2 1

Xenopus genome
by Kurtenbach, Stefan 09 Jun '16

09 Jun '16

Dear Galaxy team, First, thanks for your great work! I want to use Bowtie2 to align ChIPseq data to the Xenopus laevis genome. However, It's not listed. The tool said that if the desired genome is not in the list to contact the galaxy team, so here I am :) Could you add this? Thanks! Stefan

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Re: [galaxy-dev] How to get the encoded ID from the HistoryDatasetAssociation?
by Malcolm Tobias 08 Jun '16

08 Jun '16

Thanks Martin! With your hint and the example from graphviz.mako I was able to get this to work. Cheers, Malcolm On Wednesday, June 08, 2016 03:23:31 PM Martin Čech wrote: Hello Malcolm, encoded_id is a database row id that has been ran through this method (https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/security/__…) using the 'secret' from galaxy.ini config. You should be able to do something like this in the mako: ${trans.security.encode_id( hda.id[2] )} thank you for using Galaxy Martin On Wed, Jun 8, 2016 at 11:16 AM Malcolm Tobias <mtobias(a)wustl.edu[3]> wrote: hda.name[4] and hda.id[2] I can see various properties of thedataset, but not the encoded ID. Any suggestions on how to do this? Thanks in advance. Malcolm --Malcolm Tobias314.362.1594 ___________________________________________________________Please keep all replies on the list by using "reply all"in your mail client. To manage your subscriptions to thisand other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/[5] http://galaxyproject.org/search/mailinglists/[6] -- Malcolm Tobias 314.362.1594 -------- [1] https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/security/__… [2] http://hda.id [3] mailto:mtobias@wustl.edu [4] http://hda.name [5] https://lists.galaxyproject.org/ [6] http://galaxyproject.org/search/mailinglists/

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Any way to prime the value of a tool text field parameter dynamically?
by Dooley, Damion 08 Jun '16

08 Jun '16

I have a need to have the default value of a text parameter : <param name="statements" label="Statements" type="text" area="true" value="???"> Set dynamically, as powered by say a call to a function in <code file="tool_form.py" /> , much like a dynamic_options="get_rule_section(recipe_file)" call. Has anyone done that somehow without hacking Galaxy code? A user can then edit the text. The default depends on a previous selection (e.g. recipe_file input). Thanks, Damion

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galaxy-dev June 2016