October 2015 - galaxy-dev - lists.galaxyproject.org

search paths for custom tools
by Tony Schreiner 26 Oct '15

26 Oct '15

Beginner question, I apologize. I recently set up a galaxy server for the first time. The users of this server are installing custom tools of their own creation. Some of these tools use binaries from fastx_toolkit, and python libs from biopython. Both of these have been added from tool_shed. I have not understood yet, how to set the search path for these dependencies in the custom tools. I see the env.sh files in the tool_shed directories, but am now wondering if there is way to specify in the custom tools' xml files how to invoke the needed env.sh. Or what is the more proper way to do do this. Tony Schreiner Boston College

2 2

HTML and download links
by Sabrina Legoueix Rodriguez 23 Oct '15

23 Oct '15

Hi, I would like to generate an html output (in the .xml) in my wrapper with links to other outputs. The user wants to obtain only 1 html output file when the tool has finished to run ; and that html page should contain links to all other outputs to be downloaded (zip files). Could you please tell me if there s a way to do so in galaxy and could you please tell le how ? Thanks in advance, Best regards, -- Signature e-mail TWB Sabrina **Sabrina LEGOUEIX RODRIGUEZ** Responsable Plateau Bioinformatique Tél. : +33 (0) 5 61 28 57 92 sabrina.legoueix(a)toulouse.inra.fr <mailto:[MAIL]> www.toulouse-white-biotechnology.com <http://www.toulouse-white-biotechnology.com/> LinkedIn <https://www.linkedin.com/company/2757525h> Twitter <https://twitter.com/TWB_Biotech> TWB - Parc technologique du canal • Bâtiment NAPA CENTER B • 3, rue Ariane • 31520 Ramonville Saint-Agne Ce message et ses pièces jointes sont strictement personnels. Ils peuvent contenir des informations confidentielles. Si vous avez reçu ce message par erreur, merci d'en avertir l'expéditeur et de détruire le message et les documents joints. Toute utilisation des informations reçues par erreur est interdite. This message and the attachments are strictly personal. They may contain confidential information. If you have received this message in error, please notify the sender and delete the message and the attachments. Any use of this communication received in error is prohibited.

2 1

Deleting / deprecating an empty Tool Shed repository?
by Peter Cock 22 Oct '15

22 Oct '15

Hi all, Following the Biopython 1.66 release, I will be creating: https://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_66/ https://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_66/ Due to user error and a planemo bug [1], I accidentally created the following on the Test Tool Shed: https://testtoolshed.g2.bx.psu.edu/view/peterjc/package_biopython_1_66/ https://testtoolshed.g2.bx.psu.edu/view/peterjc/package_biopython_1_66/0000… At this point nothing has been uploaded, so I would ideally like to delete it. Failing that, I would manually deprecate it - but I can't see any action to do so - only an upload file button. (From memory there is an automatic deprecation process for empty repositories which should take care of this.) Would offering deletion be reasonable in this situation? Thanks, Peter [1] https://github.com/galaxyproject/planemo/issues/246

1 0

external authentication - empty REMOTE_USER
by Floreline TOUCHARD 22 Oct '15

22 Oct '15

Hi, I've got an issue with my external authentication configuration. I use Apache and the mod_perl modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with NIS accounts. I have the authentication form when I try to access galaxy web page. But after a successful authentication it seems that the REMOTE_USER variable is not passed to my galaxy instance. I'm connected under "@ example.org" regardless of the authentication account. That's why I think the REMOTE_USER passed to Galaxy is not 'null' but empty. I tested the value of the variable with the following php script: <?PHP foreach($_SERVER as $key_name => $key_value) { print $key_name . " = " . $key_value . "<br>"; } ?> I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value. I don't understand where my problem lies. Here is my galaxy.conf file : Listen 2208 <VirtualHost *:2208> RewriteEngine on DocumentRoot "/path/to/static" <Directory "/path/to/static"> Options +Indexes FollowSymLinks MultiViews AllowOverride None Order allow,deny Allow from all AuthType Basic AuthName "Authentifiez vous" PerlAuthenHandler Apache2::AuthenNIS PerlAuthzHandler Apache2::AuthzNIS PerlSetVar AllowAlternateAuth no require valid-user </Directory> RewriteEngine on RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}] RequestHeader set REMOTE_USER %{RU}e RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/static/style/(.*) /path/to/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*) /softhpc/galaxy/test/galaxy-master/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*) /path/to/static/$1 [L] RewriteRule ^/favicon.ico /path/to/static/favicon.ico [L] RewriteRule ^/robots.txt /path/to/static/robots.txt [L] RewriteRule ^(.*) http://localhost:2209$1 [P] </VirtualHost> Thanks in advance ! F.T

3 6

issue with install_tool_shed_repositories.py
by Steve.Mcmahon＠csiro.au 22 Oct '15

22 Oct '15

Hi, We are doing a puppet configuration for our Galaxy service and this includes installing tools with the "install_tool_shed_repositories.py" script. It seems that when we specify a revision for a tool which is not the latest we get an error e.g. /usr/bin/python /OSM/galaxy/tools/galaxy-dev-03/galaxy-dist/scripts/api/install_tool_shed_repositories.py --api xxxxxxxxxxxxx -l http://localhost --url http://toolshed.g2.bx.psu.edu/ -o devteam --name fasta_nucleotide_changer --tool-deps --repository-deps -r 2f868bfbe9de --panel-section-id NGS_QC HTTP Error 500: Internal Server Error {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0} Has anyone seen this? Shall I create an issue in Trello for it? Our work around is to use the latest revision. We'd probably like to not have to do that, however. Cheers. Steve McMahon Solution Architect and Senior System Administrator | Scientific Computing Information Management and Technology CSIRO T +61 2 6214 2968 Alt +61 4 0077 9318 steve.mcmahon(a)csiro.au<mailto:steve.mcmahon@csiro.au> | www.csiro.au 1 Wilf Crane Crescent, Yarralumla ACT 2600 PLEASE NOTE The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference. Please consider the environment before printing this email.

1 0

Spaces in GenomeSpaces file URLs from genomespace_importer tool
by Marco Ocana 21 Oct '15

21 Oct '15

Hi, I am encountering a problem executing the genomespace_importer tool using the Galaxy API. The tool works just fine to copy files in GenomeSpace into Galay a history dataset EXCEPT when the GenomeSpace file URL includes a space (" ") of any sort. Below is an example problem request (the GenomeSpace URL is public, so you should be able to try it if you like). Note that the "URL" parameter includes a couple of %20 which are supposed to url-encode the space character. *POST https://usegalaxy.org/api/tools?key=XXXXXX <https://usegalaxy.org/api/tools?key=XXXXXX>* *{* * "history_id": "039421d939e31170",* * "tool_id": "genomespace_importer",* * "inputs": {* * "URL": "https://dm.genomespace.org/datamanager/file/Home/Public/RecipeData/Sequence… <https://dm.genomespace.org/datamanager/file/Home/Public/RecipeData/Sequence…>",* * "gs-token": null* * }* *}* The job is accepted by Galaxy but eventually it fails. An HTTP error occurs during the execution of the job. I looked through the logs in GenomeSpace. Turns out that the URL being used by Galaxy to do a GET on the file is *https://gsui.genomespace.org/datamanager/v1.0/file/Home/Public/RecipeData/SequenceData_fa <https://gsui.genomespace.org/datamanager/v1.0/file/Home/Public/RecipeData/S…>X20fastaX20fastq/RNA-Seq.fastq* The "percents" are converted to X (I made the Xs bigger for emphasis). I attempted a couple of other experiments in the tool job submission, using actual space characters instead of %20. I also tried using the + instead of space. In both of these attempts, the exact same file path in the URL param was used for the GenomeSpace GET, leading to a BAD REQUEST error with the actual space character and NOT FOUND error with the + . So the question is: what kind of decoding is going on in the Galaxy genomespace_importer tool and how do I get rid of the Xs? Thanks Marco

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Re: [galaxy-dev] Tools that make datasets
by Peter van Heusden 21 Oct '15

21 Oct '15

These names have meaning in CollectedDatasetMatch: designation means designation if that exists else name name means name dbkey means dbkey ext means ext visible means visible On 21 October 2015 at 08:44, Steve Cassidy <steve.cassidy(a)mq.edu.au> wrote: > Thanks, yes that works, though I'm not really sure what the difference is > between __name__ and __designation__. They both seem to have the same > effect in my example. > > Thanks for your help. > > Steve > > > On 21 October 2015 at 16:49, Peter van Heusden <pvh(a)sanbi.ac.za> wrote: > >> Since you're using a directory, you can use one of the built in patterns: >> >> DEFAULT_EXTRA_FILENAME_PATTERN = r"primary_DATASET_ID_(?P<designation>[^_]+)_(?P<visible>[^_]+)_(?P<ext>[^_]+)(_(?P<dbkey>[^_]+))?" >> >> NAMED_PATTERNS = { >> "__default__": DEFAULT_EXTRA_FILENAME_PATTERN, >> "__name__": r"(?P<name>.*)", >> "__designation__": r"(?P<designation>.*)", >> "__name_and_ext__": r"(?P<name>.*)\.(?P<ext>[^\.]+)?", >> "__designation_and_ext__": r"(?P<designation>.*)\.(?P<ext>[^\._]+)?", >> } >> >> In terms of docs, I don't know what the future is - the Galaxy wiki or http://galaxy.readthedocs.org/en/master/ >> >> >> On 21 October 2015 at 04:26, Steve Cassidy <steve.cassidy(a)mq.edu.au> >> wrote: >> >>> Ah, thankyou, yes, I can now get results by using patterns to match the >>> output. I used your example but prepend 'simple' to the filename and then >>> searches for that with: >>> >>> <discover_datasets pattern="simple(?P<name>.*)" /> >>> this solves the problem for the sample script but not generally since in >>> general I can't predict the filenames that will be generated - this is a >>> tool for downloading data from a repository which could be text, audio or >>> video data. >>> >>> If I don't use the 'simple' prefix and omit the file extension I still >>> get my data but I also get three other files which are temporary scripts >>> generated by galaxy and placed in the working directory. So, back to >>> trying to put things in a subdirectory. It turns out that the issue I was >>> having was as you pointed out earlier, the directory attribute to >>> discover_datasets doesn't allow variables, so I need to write to a fixed >>> directory name: >>> >>> <discover_datasets pattern="(?P<name>.*)" directory="SampleDataset >>> " /> >>> This now works! >>> >>> I had thought that I'd need to use a unique directory name but since >>> galaxy runs each job in a separate directory, this isn't required. My real >>> tool now works too after following the same pattern. >>> >>> Thanks for your help. I'll see if I can write this up in a blog post. >>> >>> Steve >>> >>> >>> >>> On 21 October 2015 at 00:06, Peter van Heusden <pvh(a)sanbi.ac.za> wrote: >>> >>>> I poked around at your tool XML and the code a bit and the problem is >>>> directory="$job_name". Galaxy expects to collect files from the job's >>>> working directory - basically the current working directory the job runs >>>> in. The directory= argument doesn't have variables expanded as far as I can >>>> tell. In any event it is used in walk_over_extra_files() that is in >>>> lib/galaxy/tools/parameters/output_collect.py - if you look there you see >>>> that it is simply appended to the job's working directory. >>>> >>>> So if you use: >>>> >>>> <discover_datasets pattern="(?P<name>.*)\.txt" /> >>>> >>>> (note the < and > - this is effectively the regexp >>>> r"(?P<name>.*)\.txt" with the < and > escaped out) >>>> >>>> And alter the code so that it just writes files to the current >>>> directory, then you'll pick up the files one.txt, two,txt and three.txt. >>>> >>>> Peter >>>> >>>> On 20 October 2015 at 12:28, Steve Cassidy <steve.cassidy(a)mq.edu.au> >>>> wrote: >>>> >>>>> Sorry, it was just an example of a tool that works - the file that it >>>>> writes out is put into that directory, so I assume that's where my files >>>>> should end up too. >>>>> >>>>> Steve >>>>> >>>>> On 20 October 2015 at 21:12, Peter van Heusden <pvh(a)sanbi.ac.za> >>>>> wrote: >>>>> >>>>>> Sorry, I don't understand - what does the Upload File tool have to do >>>>>> with this? >>>>>> >>>>>> On 20 October 2015 at 11:49, Steve Cassidy <steve.cassidy(a)mq.edu.au> >>>>>> wrote: >>>>>> >>>>>>> Yes, I'm sure that's where the problem lies. Writing out to the >>>>>>> current directory doesn't work. The files get written to >>>>>>> 'job_working_directory/000/1/' but if I run the Upload File tool the result >>>>>>> is placed in 'files/000/'. I think I need to work out where to write the >>>>>>> files, I found some references to $__new_file_path__ but that doesn't seem >>>>>>> to help. >>>>>>> >>>>>>> Steve >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 20 October 2015 at 19:57, Peter van Heusden <pvh(a)sanbi.ac.za> >>>>>>> wrote: >>>>>>> >>>>>>>> I suspect that the problem might be in the <discover_datasets> >>>>>>>> then. I'm not an export on this, but "__name_and_ext__" turns into the >>>>>>>> regexp r"(?P<name>.*)\.(?P<ext>[^\.]+)?" in >>>>>>>> lib/galaxy/tools/parameters/output_collect.py, and is used by the >>>>>>>> DatasetCollector (line 358). This looks like it should match the filenames >>>>>>>> you're creating, but I'm not 100% sure how that code works. One thing I >>>>>>>> notice is the "directory" argument. If you write jobs to the current >>>>>>>> directory instead of "output_path" can you get it to work? >>>>>>>> >>>>>>>> Peter >>>>>>>> >>>>>>>> On 20 October 2015 at 09:52, Steve Cassidy <steve.cassidy(a)mq.edu.au >>>>>>>> > wrote: >>>>>>>> >>>>>>>>> Thanks Peter, >>>>>>>>> I did see that proviso somewhere but no, refreshing doesn't help. >>>>>>>>> >>>>>>>>> That page was one of those that I referred to getting to this >>>>>>>>> point. >>>>>>>>> >>>>>>>>> Steve >>>>>>>>> >>>>>>>>> On 20 October 2015 at 18:33, Peter van Heusden <pvh(a)sanbi.ac.za> >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> Just a quick check - did you refresh your history to confirm that >>>>>>>>>> the dataset *is* empty? We had the same thing at SANBI but it turns out >>>>>>>>>> that Galaxy creates an empty output collection and then only populates it >>>>>>>>>> sometime after job completion (this is a know UI bug). >>>>>>>>>> >>>>>>>>>> See: >>>>>>>>>> http://pvh.wp.sanbi.ac.za/2015/09/18/adventures-in-galaxy-output-collection… >>>>>>>>>> >>>>>>>>>> On 20 October 2015 at 08:48, Steve Cassidy < >>>>>>>>>> steve.cassidy(a)mq.edu.au> wrote: >>>>>>>>>> >>>>>>>>>>> Hi all, >>>>>>>>>>> I'm trying to understand how to write a tool that generates a >>>>>>>>>>> dataset rather than a single output file. I've tried following all of the >>>>>>>>>>> examples but I'm stuck, so I thought I would distil down the simplest >>>>>>>>>>> example I could write and ask for help here. >>>>>>>>>>> >>>>>>>>>>> So here's my example: >>>>>>>>>>> >>>>>>>>>>> https://gist.github.com/stevecassidy/0fa45ad5853faacb5f55 >>>>>>>>>>> >>>>>>>>>>> it's a simple python script that writes three files to a >>>>>>>>>>> directory named for the single input parameter. >>>>>>>>>>> >>>>>>>>>>> I think one of the problems I'm having is knowing where to write >>>>>>>>>>> the output to. I've run this under planemo serve and the job runs, creating >>>>>>>>>>> the output directory within the 'job_working_directory/000/1/SampleDataset' >>>>>>>>>>> directory, however my dataset doesn't contain anything so clearly my >>>>>>>>>>> outputs directive isn't working: >>>>>>>>>>> >>>>>>>>>>> <outputs> >>>>>>>>>>> <collection type="list" label="$job_name" name="output1"> >>>>>>>>>>> <discover_datasets pattern="__name_and_ext__" >>>>>>>>>>> directory="$job_name" /> >>>>>>>>>>> </collection> >>>>>>>>>>> </outputs> >>>>>>>>>>> >>>>>>>>>>> ($job_name is the name of the directory that is being written >>>>>>>>>>> to, SampleDataset in this case) >>>>>>>>>>> >>>>>>>>>>> Any help in getting this example working would be appreciated. >>>>>>>>>>> >>>>>>>>>>> Thanks, >>>>>>>>>>> >>>>>>>>>>> Steve >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Department of Computing, Macquarie University >>>>>>>>>>> http://web.science.mq.edu.au/~cassidy/ >>>>>>>>>>> >>>>>>>>>>> ___________________________________________________________ >>>>>>>>>>> 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/ >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Department of Computing, Macquarie University >>>>>>>>> http://web.science.mq.edu.au/~cassidy/ >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ___________________________________________________________ >>>>>>>> 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/ >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Department of Computing, Macquarie University >>>>>>> http://web.science.mq.edu.au/~cassidy/ >>>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> Department of Computing, Macquarie University >>>>> http://web.science.mq.edu.au/~cassidy/ >>>>> >>>> >>>> >>>> ___________________________________________________________ >>>> 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/ >>>> >>> >>> >>> >>> -- >>> Department of Computing, Macquarie University >>> http://web.science.mq.edu.au/~cassidy/ >>> >> >> > > > -- > Department of Computing, Macquarie University > http://web.science.mq.edu.au/~cassidy/ >

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Re: [galaxy-dev] Tools that make datasets
by Peter van Heusden 21 Oct '15

21 Oct '15

I poked around at your tool XML and the code a bit and the problem is directory="$job_name". Galaxy expects to collect files from the job's working directory - basically the current working directory the job runs in. The directory= argument doesn't have variables expanded as far as I can tell. In any event it is used in walk_over_extra_files() that is in lib/galaxy/tools/parameters/output_collect.py - if you look there you see that it is simply appended to the job's working directory. So if you use: <discover_datasets pattern="(?P<name>.*)\.txt" /> (note the < and > - this is effectively the regexp r"(?P<name>.*)\.txt" with the < and > escaped out) And alter the code so that it just writes files to the current directory, then you'll pick up the files one.txt, two,txt and three.txt. Peter On 20 October 2015 at 12:28, Steve Cassidy <steve.cassidy(a)mq.edu.au> wrote: > Sorry, it was just an example of a tool that works - the file that it > writes out is put into that directory, so I assume that's where my files > should end up too. > > Steve > > On 20 October 2015 at 21:12, Peter van Heusden <pvh(a)sanbi.ac.za> wrote: > >> Sorry, I don't understand - what does the Upload File tool have to do >> with this? >> >> On 20 October 2015 at 11:49, Steve Cassidy <steve.cassidy(a)mq.edu.au> >> wrote: >> >>> Yes, I'm sure that's where the problem lies. Writing out to the current >>> directory doesn't work. The files get written to >>> 'job_working_directory/000/1/' but if I run the Upload File tool the result >>> is placed in 'files/000/'. I think I need to work out where to write the >>> files, I found some references to $__new_file_path__ but that doesn't seem >>> to help. >>> >>> Steve >>> >>> >>> >>> On 20 October 2015 at 19:57, Peter van Heusden <pvh(a)sanbi.ac.za> wrote: >>> >>>> I suspect that the problem might be in the <discover_datasets> then. >>>> I'm not an export on this, but "__name_and_ext__" turns into the >>>> regexp r"(?P<name>.*)\.(?P<ext>[^\.]+)?" in >>>> lib/galaxy/tools/parameters/output_collect.py, and is used by the >>>> DatasetCollector (line 358). This looks like it should match the filenames >>>> you're creating, but I'm not 100% sure how that code works. One thing I >>>> notice is the "directory" argument. If you write jobs to the current >>>> directory instead of "output_path" can you get it to work? >>>> >>>> Peter >>>> >>>> On 20 October 2015 at 09:52, Steve Cassidy <steve.cassidy(a)mq.edu.au> >>>> wrote: >>>> >>>>> Thanks Peter, >>>>> I did see that proviso somewhere but no, refreshing doesn't help. >>>>> >>>>> That page was one of those that I referred to getting to this point. >>>>> >>>>> Steve >>>>> >>>>> On 20 October 2015 at 18:33, Peter van Heusden <pvh(a)sanbi.ac.za> >>>>> wrote: >>>>> >>>>>> Just a quick check - did you refresh your history to confirm that the >>>>>> dataset *is* empty? We had the same thing at SANBI but it turns out that >>>>>> Galaxy creates an empty output collection and then only populates it >>>>>> sometime after job completion (this is a know UI bug). >>>>>> >>>>>> See: >>>>>> http://pvh.wp.sanbi.ac.za/2015/09/18/adventures-in-galaxy-output-collection… >>>>>> >>>>>> On 20 October 2015 at 08:48, Steve Cassidy <steve.cassidy(a)mq.edu.au> >>>>>> wrote: >>>>>> >>>>>>> Hi all, >>>>>>> I'm trying to understand how to write a tool that generates a >>>>>>> dataset rather than a single output file. I've tried following all of the >>>>>>> examples but I'm stuck, so I thought I would distil down the simplest >>>>>>> example I could write and ask for help here. >>>>>>> >>>>>>> So here's my example: >>>>>>> >>>>>>> https://gist.github.com/stevecassidy/0fa45ad5853faacb5f55 >>>>>>> >>>>>>> it's a simple python script that writes three files to a directory >>>>>>> named for the single input parameter. >>>>>>> >>>>>>> I think one of the problems I'm having is knowing where to write the >>>>>>> output to. I've run this under planemo serve and the job runs, creating the >>>>>>> output directory within the 'job_working_directory/000/1/SampleDataset' >>>>>>> directory, however my dataset doesn't contain anything so clearly my >>>>>>> outputs directive isn't working: >>>>>>> >>>>>>> <outputs> >>>>>>> <collection type="list" label="$job_name" name="output1"> >>>>>>> <discover_datasets pattern="__name_and_ext__" >>>>>>> directory="$job_name" /> >>>>>>> </collection> >>>>>>> </outputs> >>>>>>> >>>>>>> ($job_name is the name of the directory that is being written to, >>>>>>> SampleDataset in this case) >>>>>>> >>>>>>> Any help in getting this example working would be appreciated. >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> Steve >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Department of Computing, Macquarie University >>>>>>> http://web.science.mq.edu.au/~cassidy/ >>>>>>> >>>>>>> ___________________________________________________________ >>>>>>> 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/ >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Department of Computing, Macquarie University >>>>> http://web.science.mq.edu.au/~cassidy/ >>>>> >>>> >>>> >>>> ___________________________________________________________ >>>> 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/ >>>> >>> >>> >>> >>> -- >>> Department of Computing, Macquarie University >>> http://web.science.mq.edu.au/~cassidy/ >>> >> >> > > > -- > Department of Computing, Macquarie University > http://web.science.mq.edu.au/~cassidy/ >

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recurring issues with revisions of packages from toolshed
by Sarah DIEHL 20 Oct '15

20 Oct '15

Dear all, I continuously have several issues with tool dependency packages from the toolshed and their revisions. It looks like the tools I install have requirements for different revisions of the same package_xy repository. What I end up with quite often is having the same package installed in multiple revisions (see attached "galaxytools_multiple_revisions.jpg" screenshot). When I then update the older revision, it's still listet twice and additionally the tool that had the older one as a dependency now says it's missing a repository dependency. Although this is already quite annoying and creates a mess within the tool list, I could live with it. However, sometimes it completely messes up revisions. In the second attached screenshot (numpy_revision_issue.jpg) you can see that this numpy repository thinks it is revision "300877695495", but it's actual location has revision "8b3a5c7061d8". This causes tools that depend on revision "300877695495" to think it's there, but when the dependency is resolved at runtime of the tool, numpy is not found (since it's location is in a different revision's folder) and the run fails. As you can also see from the screenshot, resetting the metadata doesn't do anything about this. Also reinstalling doesn't work, since the database keeps the faulty record and uses it upon reinstallation. I think it's a problem that when I install tools that have outdated revisions of a package repository as a dependency, they don't recognize that a newer version is available (and already installed), but instead insist on installing the older revision, too. I don't understand why they even have this strict requirement on a specific version of a package repo, and not just the version of the tool inside. Btw. I also noticed that the installation of R packages (e.g. in package_dexseq_1_14) silently fails. Some of the requirements and also the dexseq R package itself failed the installation, but Galaxy didn't recognize any error and it still showed up as "Installed". Best regards, Sarah ---- Sarah Diehl HPC System Administrator UNIVERSITÉ DU LUXEMBOURG LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE Campus Belval | Biotech II 6, avenue du Swing L-4371 Belvaux T +352 46 66 44 5360 sarah.diehl(a)uni.lu<mailto:sarah.diehl@uni.lu> http://lcsb.uni.lu<http://lcsb.uni.lu/> ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. -----

4 9

Tools that make datasets
by Steve Cassidy 20 Oct '15

20 Oct '15

Hi all, I'm trying to understand how to write a tool that generates a dataset rather than a single output file. I've tried following all of the examples but I'm stuck, so I thought I would distil down the simplest example I could write and ask for help here. So here's my example: https://gist.github.com/stevecassidy/0fa45ad5853faacb5f55 it's a simple python script that writes three files to a directory named for the single input parameter. I think one of the problems I'm having is knowing where to write the output to. I've run this under planemo serve and the job runs, creating the output directory within the 'job_working_directory/000/1/SampleDataset' directory, however my dataset doesn't contain anything so clearly my outputs directive isn't working: <outputs> <collection type="list" label="$job_name" name="output1"> <discover_datasets pattern="__name_and_ext__" directory="$job_name" /> </collection> </outputs> ($job_name is the name of the directory that is being written to, SampleDataset in this case) Any help in getting this example working would be appreciated. Thanks, Steve -- Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy/

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