Re: [galaxy-dev] Problem using FastQC in Galaxy
I attempted to install fastqc via the tool shed, and got an error. The log information is listed below. The main error appears to be too many values to unpack. 152.2.204.5 - - [05/Jan/2015:09:09:00 -0400] GET /admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=ca249a25748b71a3changeset_revisions=0b201de108b9 HTTP/1.1 500 - https://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=ca249a25748b71a3changeset_revision=0b201de108b9; Mozilla/5.0 (X11; Linux x86_64; rv:34.0) Gecko/20100101 Firefox/34.0 Error - type 'exceptions.ValueError': too many values to unpack URL: https://galaxy.its.unc.edu/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=ca249a25748b71a3changeset_revisions=0b201de108b9 File '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/base.py', line 185 in handle_request body = method( trans, **kwargs ) File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 216 in decorator return func( self, trans, *args, **kwargs ) File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1345 in prepare_for_install shed_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ) File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/util/shed_util.py', line 601 in get_dependencies_for_repository installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple ) File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/util/shed_util.py', line 715 in get_installed_and_missing_repository_dependencies_for_new_install tool_shed, name, owner, changeset_revision = rd_tup ValueError: too many values to unpack Configuration - __file__: '/nas02/apps/galaxy-prod/galaxy-dist/universe_wsgi.ini' admin_users: 'roac...@email.unc.edu,kel...@email.unc.edu,mwald...@email.unc.edu,jen...@email.unc.edu' allow_user_dataset_purge: 'True' database_connection: 'postgres://galaxy@localhost/galaxy' database_engine_option_server_side_cursors: 'True' database_engine_option_strategy: 'threadlocal' debug: 'False' default_cluster_job_runner: 'drmaa://-q pgalaxy_q -M 4190 /' enable_quotas: 'True' enable_tracks: 'True' file_path: '/proj/galaxy' ftp_upload_dir: 'database/ftp' ftp_upload_site: 'galaxy.its.unc.edu:2021' here: '/nas02/apps/galaxy-prod/galaxy-dist' job_working_directory: '/proj/galaxy/job_working_directory' len_file_path: 'tool-data/shared/ucsc/chrom' library_import_dir: '/proj/seq/galaxy' local_job_queue_workers: '10' nglims_config_file: 'tool-data/nglims.yaml' remote_user_maildomain: 'email.unc.edu' retry_job_output_collection: '30' start_job_runners: 'drmaa' static_cache_time: '360' static_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/' static_enabled: 'True' static_favicon_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/favicon.ico' static_images_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/images' static_scripts_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/scripts/' static_style_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/june_2007_style/blue' tool_config_file: 'tool_conf.xml,shed_tool_conf.xml' tool_dependency_dir: '../tool_dependencies' tool_path: 'tools' use_interactive: 'False' use_nglims: 'False' use_remote_user: 'True' WSGI Variables -- application: paste.recursive.RecursiveMiddleware object at 0x1fa05fd0 original_wsgi.url_scheme: 'http' paste.cookies: (SimpleCookie: VCLACTIVENODE='12' VCLAUTH='laCke775oUL18xKNIRgrIGOkWV8TDHKwq647BxYTcK1NkdOlvh0%2B8glvFC%2BdvpkoiYg7qttH2AXyWKGmw2aqWVJKp%2BeLJFauRWutlotbDElWn6CfZYeYesGHlWgWMnWbxAW8EYmsmecDsM0xV3KW5%2BFrMdBpDdseXYKCEXzpIIvvwp7F8gX%2BU%2BEUjPE3lb4JzGWf3Ie9XgfEqlPycbiJXPHXCrsGkanB3NXDzJJeUwe9PFO5bc0%2BA1vP7X3YxYdfjLxVAK9ZVqv8tpVwkyh26Mc%2BJ6ei5j9oYmOgQSGdoBuI3y6JmQuivN0z0I6%2FdFy1LBAH74Ri%2FZMgdL7%2Bgjj79A%3D%3D' VCLLOCALE='en_US' VCLSKIN='default' __unam='74abf65-13ed3051d32-51a5d500-40'
[galaxy-dev] January 2015 Galaxy News!
Happy New Year from the Galaxy Project! January https://wiki.galaxyproject.org/GalaxyUpdates/2015_01 brings lots of Galaxy related news https://wiki.galaxyproject.org/GalaxyUpdates/2015_01, including - 63 new papers https://wiki.galaxyproject.org/GalaxyUpdates/2015_01#New_Papers, including 4 highlighted papers, referencing, using, extending, and implementing Galaxy. (There are now over 2000 papers in the Galaxy CiteULike library http://www.citeulike.org/group/16008/.) - *GCC2015 Training Day Topic Nominations close this week https://wiki.galaxyproject.org/GalaxyUpdates/2015_01#Training_Day_Topic_Nominations_Close_6_January!* - GCC2015 needs sponsors https://wiki.galaxyproject.org/GalaxyUpdates/2015_01#Call_for_Sponsors! - Other upcoming events https://wiki.galaxyproject.org/GalaxyUpdates/2015_01#Other_Events on two continents - Job openings at 7 organizations https://wiki.galaxyproject.org/GalaxyUpdates/2015_01#Who.27s_Hiring - *GalaxyAdmins is back https://wiki.galaxyproject.org/GalaxyUpdates/2015_01#GalaxyAdmins_is_back.21!* Please tell what times work best for the next meetup. - Two new public servers https://wiki.galaxyproject.org/GalaxyUpdates/2015_01#New_Public_Servers : MetaNET https://wiki.galaxyproject.org/GalaxyUpdates/2015_01#MetaNET and VectorBase https://wiki.galaxyproject.org/GalaxyUpdates/2015_01#VectorBase_Galaxy. - Three new Galaxy Training Resources https://wiki.galaxyproject.org/GalaxyUpdates/2015_01#Galaxy_Community_Hubs - Over 30 new and updated ToolShed repositories from 12 contributors https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#ToolShed_Contributions - And, other news https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#Other_News too. Dave Clements and the Galaxy Team https://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Problem using FastQC in Galaxy
Hi Ryan, I have tried to collect a minimal set of dependencies you need to have installed: https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList And we have a Galaxy Docker container that is working and should define and test a fresh Galaxy installation: https://github.com/bgruening/docker-galaxy-stable Please also have a look at the Galaxy playbook: https://github.com/galaxyproject/usegalaxy-playbook This defines a installation and deployment strategy of Galaxy for several platforms. I don't think that the Galaxy project is going to focus on one single platform. But this is only my opinion. I think one of Galaxy strength is, that it is working on everything besides Windows (without docker). Cheers, Bjoern Am 05.01.2015 um 23:36 schrieb Ryan G: I hate to hijack this thread, but I was thinking about this over the holiday in how we are going to maintain a local up to date copy of Galaxy ourselves. One thought would be to standardize on a single supported platform aka an Amazon instance and make sure everything works on that single platform. This frees you from having to support many different platforms and versions. Have you guys given this some thought? On Mon, Jan 5, 2015 at 12:05 PM, Nate Coraor n...@bx.psu.edu wrote: Hi Michael, I understand your frustration in this regard. We do make an effort to respond to and fix issues that people encounter when upgrading Galaxy releases. We've also made pretty significant strides in increasing the quality of our releases, including a feature freeze for at least 2 weeks prior to each release. The galaxy-dev mailing list is fairly active, as is our IRC channel (#galaxyproject on Freenode) for more real-time help. If you're not familiar with the Galaxy News Briefs, these are the primary means of communicating the changes you should expect to see between Galaxy releases and any config changes that might be necessary between releases: https://wiki.galaxyproject.org/DevNewsBriefs We also recommend having a Test/QA Galaxy server (or cloning your production Galaxy instance) to test an upgrade before deploying it on your production instance(s) so most problems can be caught beforehand. Unfortunately, due to the wide range of platforms, deployment scenarios, site-specific factors, and large scope of Galaxy functionality, we can't catch all potential issues. I don't think this is outside the rate typically experienced with major releases of large open source software, but it is still frustrating when it occurs. That said, we'll do our best to assist and improve documentation when you do encounter upgrade problems. --nate ___ 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/
[galaxy-dev] Text file busy
I get this error occasionally: /bin/sh: 1: /opt/galaxy/web/database/job_working_directory/000/100/galaxy_100.sh: Text file busy When this occurs, the step fails outright. Resubmitting the step resolves the issue and things run no problem. If this error appears early in a long workflow, I have to manually resubmit ALL dependent steps... what a pain! Perhaps this is something the Galaxy job scheduler can look out for, flush() the system, sleep() a second or two to let the file write and close, and then rerun. A more fault-tolerant way of running workflows without unnecessary human intervention. Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Problem using FastQC in Galaxy
I hate to hijack this thread, but I was thinking about this over the holiday in how we are going to maintain a local up to date copy of Galaxy ourselves. One thought would be to standardize on a single supported platform aka an Amazon instance and make sure everything works on that single platform. This frees you from having to support many different platforms and versions. Have you guys given this some thought? On Mon, Jan 5, 2015 at 12:05 PM, Nate Coraor n...@bx.psu.edu wrote: Hi Michael, I understand your frustration in this regard. We do make an effort to respond to and fix issues that people encounter when upgrading Galaxy releases. We've also made pretty significant strides in increasing the quality of our releases, including a feature freeze for at least 2 weeks prior to each release. The galaxy-dev mailing list is fairly active, as is our IRC channel (#galaxyproject on Freenode) for more real-time help. If you're not familiar with the Galaxy News Briefs, these are the primary means of communicating the changes you should expect to see between Galaxy releases and any config changes that might be necessary between releases: https://wiki.galaxyproject.org/DevNewsBriefs We also recommend having a Test/QA Galaxy server (or cloning your production Galaxy instance) to test an upgrade before deploying it on your production instance(s) so most problems can be caught beforehand. Unfortunately, due to the wide range of platforms, deployment scenarios, site-specific factors, and large scope of Galaxy functionality, we can't catch all potential issues. I don't think this is outside the rate typically experienced with major releases of large open source software, but it is still frustrating when it occurs. That said, we'll do our best to assist and improve documentation when you do encounter upgrade problems. --nate ___ 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/
Re: [galaxy-dev] Mercurial is out of date for Toolshed
Thanks. Is there an alternative way I can install tools from the Toolshed? This problem pretty much renders the toolshed unusable for me... On Mon, Jan 5, 2015 at 11:14 AM, John Chilton jmchil...@gmail.com wrote: It is certainly the case that Galaxy should be using the latest version of mercurial given a number of high profile bugs with older versions. Unfortunately it doesn't seem possible to just drop the new version it - there are some API changes that prevent Galaxy from loading when doing this and the number of people who can add new eggs to Galaxy is low. I have created a Trello card to track this issue: https://trello.com/c/9A9uIav0 Let us know if you happen to find a workaround for this issue. -John On Mon, Dec 22, 2014 at 2:55 PM, Ryan G ngsbioinformat...@gmail.com wrote: I've been trying to track down why I can't get anything from the toolshed installed and finally have it figured out. Whenever I tried to install anything I always got an Error with no explanation of what the error was. After enabling Debug messages into the log file, I see the error is: tool_shed.util.hg_util DEBUG 2014-12-22 14:47:48,910 Error cloning repository: httpsconnection instance has no attribute '_set_hostport' I googled around and found out this is a known bug/issue with older version of Mercurial and was fixed in v3. I added a line to hg_util.py to see where it picks up hg. Its using version 2.2.3. Indeed, one of the eggs downloaded by Galaxy is mercurial-2.2.3. I have the newest version of mercurial installed in my site-packages folder but I guess that's not what galaxy wants. So my question is, how do I get Galaxy to use the latest version of Mercurial? And, Why did it download an older version? ___ 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/
Re: [galaxy-dev] Mercurial is out of date for Toolshed
Hi Ryan, unfortunately not (yet). But I'm really surprised you are getting this error. It working for me and in our docker containers and other deployments. Can we try to detect the root cause of this error? Do you have conflicting mercurial version. Cheers, Bjoern Thanks. Is there an alternative way I can install tools from the Toolshed? This problem pretty much renders the toolshed unusable for me... On Mon, Jan 5, 2015 at 11:14 AM, John Chilton jmchil...@gmail.com wrote: It is certainly the case that Galaxy should be using the latest version of mercurial given a number of high profile bugs with older versions. Unfortunately it doesn't seem possible to just drop the new version it - there are some API changes that prevent Galaxy from loading when doing this and the number of people who can add new eggs to Galaxy is low. I have created a Trello card to track this issue: https://trello.com/c/9A9uIav0 Let us know if you happen to find a workaround for this issue. -John On Mon, Dec 22, 2014 at 2:55 PM, Ryan G ngsbioinformat...@gmail.com wrote: I've been trying to track down why I can't get anything from the toolshed installed and finally have it figured out. Whenever I tried to install anything I always got an Error with no explanation of what the error was. After enabling Debug messages into the log file, I see the error is: tool_shed.util.hg_util DEBUG 2014-12-22 14:47:48,910 Error cloning repository: httpsconnection instance has no attribute '_set_hostport' I googled around and found out this is a known bug/issue with older version of Mercurial and was fixed in v3. I added a line to hg_util.py to see where it picks up hg. Its using version 2.2.3. Indeed, one of the eggs downloaded by Galaxy is mercurial-2.2.3. I have the newest version of mercurial installed in my site-packages folder but I guess that's not what galaxy wants. So my question is, how do I get Galaxy to use the latest version of Mercurial? And, Why did it download an older version? ___ 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/
Re: [galaxy-dev] Problem with Biopython
On Tue, Jan 6, 2015 at 12:23 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Yes ;) Are you writing your own tool, or trying to install someone else's? There are two basic options, (1) Install Biopython into the default Python used when jobs are run. Simple, but manual - and you can only have one version. This is actually what we are still doing on our local Galaxy since we started before the second option as available. (2) Install Biopython via the ToolShed, using the dependency mechanism. This allows multiple versions of Biopython (or any Python library) to be installed in parallel, and Galaxy does the setup to ensure the declared dependency is on the Python path when your script is run. e.g. https://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss declares a dependency on: https://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_62 (which in turn depends on NumPy etc). This reminds me, we are overdue to create a Galaxy ToolShed package for Biopython 1.65, I must do that... Done, https://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_65 And for tool developers on the TestToolShed too, https://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_65 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] GCC2015 Training Day Topic Nominations are Open through January 6
Hello all, Just a reminder that GCC2015 Training Day Topic Nominations *close Tuesday, 6 January, which might be today by the time you see this. *See the Training Day http://gcc2015.tsl.ac.uk/training-day/ page for what's been nominated so far, and for a link to the nomination form. If you want to cover something, or want something covered, then please submit your idea *now.* Thanks, GCC2015 Organising Committee http://gcc2015.tsl.ac.uk/organisers On Tue, Dec 9, 2014 at 7:36 PM, Dave Clements cleme...@galaxyproject.org wrote: Hello all, GCC2015 Training Day http://gcc2015.tsl.ac.uk/training-day/ topics are nominated by you http://bit.ly/gcc2015tdnom, the Galaxy Community. Please take a few minutes to nominate a topic. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one. If you are looking for ideas, see the topics nominated in 2013 http://bit.ly/1i2j1gN and 2014 http://bit.ly/1s6NtMN, and the Events https://wiki.galaxyproject.org/Events and the Events Archives https://wiki.galaxyproject.org/Events/Archive pages. Nominated topics will be published on the Training Day http://gcc2015.tsl.ac.uk/training-day/ page as they come in. *Nominations close 6 January*. Topics will be compiled into a uniform list by the GCC2015 Organising Committee http://gcc2015.tsl.ac.uk/organisers, and topics will be voted on by the Galaxy Community 12-23 January. Topics will then be selected and scheduled based on topic interest, and the organisers' ability to confirm instructors for each session. Some very popular sessions may be scheduled more than once. The final schedule will be posted before registration opens. Cheers, GCC2015 Organising Committee http://gcc2015.tsl.ac.uk/organisers -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] galaxy.tools.parameters.basic.RuntimeValue not str
It looks like the workflow submission code was unable to map your
parameter reference_genome|index to the correct tool runtime value.
Is there any chance you can post the tool and/or the workflow? Also -
I am assuming here the tool_id is mapper_easy - is that correct?
-John
On Fri, Jan 2, 2015 at 10:26 AM, Pandori n pandorin...@gmail.com wrote:
Hi all!
Maybe somebody faced with this problem:
1) in my wf used tool with:
u'model_class': u'Conditional',
u'type': u'conditional',
u'name': u'reference_genome'}],
2) when i run wf via web - all ok, and on a second step:
Select a reference genome is test (in view details)
But, when i run wf via api:
param = {u'mapper_easy' :{u'param': u'reference_genome|index', u'value':
u'test'}}
nuser.workflows.run_workflow(workflow_id=wf_id, dataset_map=dataset_map,
params=param, history_id=hist_id)
wf started and on a second step is failed... In details:
Select a reference genome is galaxy.tools.parameters.basic.RuntimeValue
object at 0x7f5374266850
Any help is appreciated. Thanks!
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Re: [galaxy-dev] Problem using FastQC in Galaxy
Hi, why do you need biopython for FASTQC? You can install biopython from the ToolShed and can depend on it: https://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_64 Cheers, Bjoern Am 05.01.2015 um 19:01 schrieb Alfredo Guilherme Silva Souza: Has anyone used the Biopython in Galaxy ? *Traceback (most recent call last):* * File /home/steve/galaxy-dist/tools/molecular_dynamics/gromacs.py, line 10, in module* *import Bio.PDB.PDBParser* *ImportError: No module named Bio.PDB.PDBParser* Researching I saw that I have to work with eggs in the Galaxy. Has anyone done this with Biopython? Is it really necessary? 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: 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/
Re: [galaxy-dev] Create a package with binaries
I could be wrong but I think the install tag should have some sort of download action - I don't think tools are actually stuck in $INSTALL_DIR like this - $INSTALL_DIR is where you can move or compile downloaded files to. You might want to try $REPOSITORY_INSTALL_DIR instead of $INSTALL_DIR - but really if you are going to just stick an application next to your tool wrapper like this (I would consider this an anti-pattern) I would just set your PATH in mytool.sh and not worry about the tool shed install stuff at all. Maybe add something like PATH=`dirname $0`/bin:$PATH export PATH To the wrapper mytool.sh. As I mentioned - I think bundling applications with tools like this is something of an anti-pattern even if you can make it work. The best practice here would be to try to separate packages with binaries from repositories that contain tools and create a format package_mytools repository that is just responsible for installing the binary mytool. Hopefully this helps, -John On Tue, Dec 16, 2014 at 9:43 AM, KRESS Arnaud (ESP) akr...@unistra.fr wrote: Hi gentlemen, I am currently struggling to create a custom package (to share via a toolshed) that would include a tool definition file and the associated binary. Once installed, I can launch a job but I get the following error message: mytool.sh: line 14: mytool: unknown command It seems that the PATH was not correctly set. What am I doing wrong ? My directory tree in my package: . ├── mytool.sh ├── mytool.xml ├── bin │ └── mytool └── tool_dependencies.xml Here is my tool_dependencies.xml file content: ?xml version=1.0? tool_dependency package name=mytool version=1.0 install version=1.0 actions action type=set_environment environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readme /readme /package /tool_dependency Thank you, AK ___ 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/
