[galaxy-dev] Trimmomatic wrapper for Galaxy

2014-11-28 Thread Peter Cock
Hi Simon, I was looking for a Trimmomatic wrapper for Galaxy (which I have thus far only used at the command line outside of Galaxy), and while there does not seem to be one in the main Tool Shed, I see you have been working on this over on the Test Tool Shed:

[galaxy-dev] Repository dependency definitions broken on Test Tool Shed

2014-12-10 Thread Peter Cock
Hi all, The Repository dependency definitions link is working on the Main Tool Shed, but fails with the following exception on the Test Tool Shed: URL: http://testtoolshed.g2.bx.psu.edu/repository/browse_repository_dependencies File

Re: [galaxy-dev] Tool Tests failing with Exception: History in error state.

2015-01-30 Thread Peter Cock
3618b7a91e23096ecf7ce5842c1e16c749251a4d . Nicola Il 30.01.2015 17:36 Peter Cock ha scritto: Retitling thread, On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks Dave, The good news is yes, the tests are running again on the Test Tool Shed (although

[galaxy-dev] Tool Tests failing with Exception: History in error state.

2015-01-30 Thread Peter Cock
Retitling thread, On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks Dave, The good news is yes, the tests are running again on the Test Tool Shed (although not the main Tool Shed yet), and many of my tools now have successful test results from last night

Re: [galaxy-dev] Tool development - Selecting a single item from input dataset.

2015-01-20 Thread Peter Cock
I think this is the (relatively new) Galaxy ability to automatically run N copies of your tool given N input files, making N outputs and is related to the collections work. (This is possible if your tool takes a single input file) Peter On Tue, Jan 20, 2015 at 6:17 PM, Vimalkumar Velayudhan

Re: [galaxy-dev] Tool test failure - I could use some help...

2015-02-12 Thread Peter Cock
On Thu, Feb 12, 2015 at 2:41 AM, Dooley, Damion damion.doo...@bccdc.ca wrote: I was trying to track down why an attempt to test my tool is eventually failing with: ValueError: No such test TestForTool_ffp_phylogeny There are at least two reasons that can happen. (a) The tool wasn't loaded

Re: [galaxy-dev] problems splitting

2015-02-12 Thread Peter Cock
Hi Roberto, It looks like this is a known issue with FASTQ splitting, https://trello.com/c/qRHLFSzd/1522-issues-with-tasked-jobs-parallelism I originally broke it during a refactor, but it looks like the discussion died about that that method was meant to do (e.g. FQTOC = FASTQ table of

[galaxy-dev] test/base/twilltestcase.py - Converting local (test-data) bam to sam failed

2015-01-27 Thread Peter Cock
Hi all, I have a query about a failing tool test on the Tool Shed, where it seems Galaxy is trying to convert both the expected BAM output and the tool's BAM output into SAM for comparison - but this fails. https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad 2015-01-27 02:13:51 ... Tool

Re: [galaxy-dev] Nothing being tested on Test and main Tool Shed?

2015-01-27 Thread Peter Cock
On Wed, Jan 7, 2015 at 2:07 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, After fixing a number of issues, it appears that the tests are now running as they should. I'll keep an eye on the test framework in case any new errors crop up. --Dave B. Thanks Dave, Yes, the good news is

Re: [galaxy-dev] Nothing being tested on Test and main Tool Shed?

2015-01-27 Thread Peter Cock
On Tue, Jan 27, 2015 at 11:32 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Jan 7, 2015 at 2:07 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, After fixing a number of issues, it appears that the tests are now running as they should. I'll keep an eye on the test framework in case

Re: [galaxy-dev] Nothing being tested on Test and main Tool Shed?

2015-01-30 Thread Peter Cock
On Fri, Jan 30, 2015 at 2:07 PM, Dannon Baker dannon.ba...@gmail.com wrote: On Fri Jan 30 2015 at 5:36:29 AM Peter Cock https://toolshed.g2.bx.psu.edu/repository/get_functional_test_rss?owner=peterjcstatus=all Internal Server Error ... Trello issue logged, https://trello.com/c

Re: [galaxy-dev] Problem with Biopython

2015-01-05 Thread Peter Cock
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

Re: [galaxy-dev] FastQC wrapper not seeing files at gzipped

2015-01-12 Thread Peter Cock
? On Mon, Jan 12, 2015 at 12:14 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Ah. Then this is more subtle... are you using the library import option where Galaxy just symlinks to existing files? I thought that was not possible with gzipped files (for the reasons given below). Perhaps

Re: [galaxy-dev] Tool Development DELLY

2015-01-12 Thread Peter Cock
metadata, that seemed to be my issue. The tool works now though! Thanks so much, Marco On 2015-01-09 7:13 PM, Peter Cock p.j.a.c...@googlemail.com javascript:; wrote: I think the symlink approach is best, see for example the Python wrapper script I used here for samtools idxstats

Re: [galaxy-dev] FastQC wrapper not seeing files at gzipped

2015-01-12 Thread Peter Cock
, Jan 12, 2015 at 4:52 PM, Ryan G ngsbioinformat...@gmail.com wrote: Galaxy is not decompressing the file. The file is linked to on the filesystem. On Mon, Jan 12, 2015 at 10:28 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Ryan, The problem isn't Galaxy stripping the extension, rather

[galaxy-dev] Problems installing package_bx_python_0_7 from Tool Shed

2015-03-19 Thread Peter Cock
Hello all, I'm trying to install the intersect tool from the main Tool Shed, https://toolshed.g2.bx.psu.edu/view/devteam/intersect One of the dependencies fails to install, with the cryptic message Initializing repository installation failed [OK]:

Re: [galaxy-dev] Comment on Training Documentation

2015-03-13 Thread Peter Cock
On Fri, Mar 13, 2015 at 12:23 AM, Martin Čech mar...@bx.psu.edu wrote: Your tutorial looks great Damion! Thank you for sharing. I am not sure about the vocabulary you are trying to estabilish though (update vs revision). I understand what you mean but I would just stick with 'If the tool

Re: [galaxy-dev] Workflow bug when *.loc entries are missing

2015-03-31 Thread Peter Cock
On Tue, Mar 31, 2015 at 11:31 AM, Peter Cock p.j.a.c...@googlemail.com wrote: ... Summary: Workflow requesting key entry xxx from example.loc (a) example.loc empty, gets empty path, fails cleanly. (b) example.loc contains xxx, gets correct path, works. (c) example.loc non empty but lacks xxx

[galaxy-dev] Workflow bug when *.loc entries are missing

2015-03-31 Thread Peter Cock
Hi all, I was testing a new workflow which I developed on the current stable release, Galaxy 15.03, and uploaded to the Tool Shed yesterday: https://github.com/peterjc/galaxy_blast/tree/master/workflows/blast_top_hit_species http://toolshed.g2.bx.psu.edu/view/peterjc/blast_top_hit_species I

Re: [galaxy-dev] Workflow bug when *.loc entries are missing

2015-04-01 Thread Peter Cock
On Wed, Apr 1, 2015 at 11:29 AM, Saket Choudhary sake...@gmail.com wrote: On 1 April 2015 at 02:06, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Mar 31, 2015 at 6:12 PM, John Chilton jmchil...@gmail.com wrote: I think it is probably a pair of bugs you are seeing: ... The fix

[galaxy-dev] Installing workflows from the Tool Shed is very confusing

2015-04-01 Thread Peter Cock
Hello all, I've been playing with the Tool Shed lately for publishing Galaxy workflows - and realised the download process is still very complicated, especially the final hurdle - importing the workflow in order to actually use it. For the following example I am starting from a clean state - an

[galaxy-dev] Multiple-select checkbox parameters not using default values

2015-03-27 Thread Peter Cock
Hi all, Unfortunately it appears that the new-look check box controls are wrongly defaulting to ticking the first item rather than following the defaults given. This is a recent regression which I noticed on updating our production Galaxy to the 15.03 release which included a number of visual

Re: [galaxy-dev] value_from_basic - KeyError: 'base_name', was: Tests not being run on toolsheds?

2015-03-23 Thread Peter Cock
.bx.psu.edu/view/peterjc/mummer I have not yet spotted any pattern in this division. (However this is clearly not linked to the test expect_failure test I'd added to the sample_seqs tool, as I speculated last week.) Regards, Peter On Wed, Mar 18, 2015 at 2:14 PM, Peter Cock p.j.a.c...@googlemail.com

Re: [galaxy-dev] test/base/twilltestcase.py - Converting local (test-data) bam to sam failed

2015-03-23 Thread Peter Cock
On Mon, Mar 23, 2015 at 1:41 PM, John Chilton jmchil...@gmail.com wrote: Hey Peter, Thanks for continuing to apply pressure on these issues. I have pushed some logging into Galaxy's development branch (https://github.com/galaxyproject/galaxy/commit/8cb06d7fc2913b4d83ca01b50d76e9607bbe379d)

[galaxy-dev] Tool tests failing on Main Tool Shed with Exception: Job in error state.

2015-03-03 Thread Peter Cock
Hello all, Good news - automated testing on the Galaxy Tool Shed seems to be mostly working again (after a period of trouble in the New Year). Thanks Dave B. et al, I'm sure this has been a lot of effort behind the scenes. I'm looking forward to getting a clean sweep of passing tests again... I

Re: [galaxy-dev] Galaxy tool shed alert for new repository named blast_reporting

2015-03-03 Thread Peter Cock
Hi Damion, I see your blast_reporting tool is now on the Main Tool Shed. https://toolshed.g2.bx.psu.edu/view/damion/blast_reporting I am a little confused about your tabular output options: option value=std selected=TrueStandard 12 columns/option option value=std+seqsStandard 12 columns +

Re: [galaxy-dev] RFC: new param attribute for Galaxy tool XML

2015-03-03 Thread Peter Cock
Hi Björn, Command line arguments are often case sensitive (e.g. samtools switches), but are Galaxy parameter names? Peter On Sat, Feb 28, 2015 at 9:11 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi all, we are planning to work on a project to implement a Galaxy fuse based shell.

Re: [galaxy-dev] Tool Testing: field inputs that occur inside repeat tag - resolved

2015-02-28 Thread Peter Cock
On Fri, Feb 27, 2015 at 10:36 PM, Dooley, Damion damion.doo...@bccdc.ca wrote: Yay, with your tip, galaxy direct tests now work with tool_conf.xml AND data table in place! Galaxy DOC person: please update https://wiki.galaxyproject.org/Admin/RunningTests to state that tool_conf.xml.sample

[galaxy-dev] $GALAXY_TEST_DB_TEMPLATE failing with KeyError: VerNum(127)

2015-02-27 Thread Peter Cock
Hi all, I've been using the SQLite template database feature to speed up functional testing. Rather than starting for the initial schema and applying all the incremental changes (as done when installing a fresh Galaxy instance), this lets the test suite start with a recent version of the

Re: [galaxy-dev] Tool Testing: field inputs that occur inside repeat tag - semi resolved.

2015-02-27 Thread Peter Cock
On Fri, Feb 27, 2015 at 8:58 PM, Dooley, Damion damion.doo...@bccdc.ca wrote: First, hey Peter, thanks for input! I'd seen the explicit piping before, couldn't remember its format though; I will switch to it. Well, after a morning of testing, I see the test system is actually finding the

[galaxy-dev] Serving Galaxy at a sub directory - symptoms without filter-with = proxy-prefix

2015-02-25 Thread Peter Cock
Hi all, TL:DR abstract: Forgetting the filter-with = proxy-prefix gives very confusing results. Hopefully this email will help someone else who made the same configuration mistake. -- As part of trying out the new (still in beta) Galaxy via git on GitHub (rather than via hg on BitBucket), I am

Re: [galaxy-dev] Serving Galaxy at a sub directory - symptoms without filter-with = proxy-prefix

2015-02-25 Thread Peter Cock
On Wed, Feb 25, 2015 at 12:26 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, TL:DR abstract: Forgetting the filter-with = proxy-prefix gives very confusing results. Hopefully this email will help someone else who made the same configuration mistake. And as a follow up, having fixed

Re: [galaxy-dev] tophat error

2015-02-24 Thread Peter Cock
On Tue, Feb 24, 2015 at 6:31 AM, Michael Thon mike.t...@gmail.com wrote: The main problem for me was that I was not aware that the tophat tool had a dependency on a command line tool outside of galaxy installation. I see in the admin interface that tophat has a dependency on samtools of type

Re: [galaxy-dev] tophat error

2015-02-24 Thread Peter Cock
On Tue, Feb 24, 2015 at 9:19 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Am 24.02.2015 um 10:03 schrieb Peter Cock: ... So far so good, but at that point Galaxy tries to index the BAM file itself. This happens for any BAM file, regardless of the tool which created it - and simply

Re: [galaxy-dev] ValueError: Attribute 'fields' does not accept objects of type type 'list'

2015-02-24 Thread Peter Cock
On Tue, Feb 24, 2015 at 2:57 PM, Dannon Baker dannon.ba...@gmail.com wrote: Hi Peter, Yes, this is a known recent issue that I'm actually at work fixing right now. -Dannon Great - I'll ignore this for now (it appears harmless for what I want to do today). Thanks, Peter

[galaxy-dev] ValueError: Attribute 'fields' does not accept objects of type type 'list'

2015-02-24 Thread Peter Cock
Hi all, I'm trying the (BETA 2) GitHub repository with a view to switching from hg for my Galaxy development. There are a couple of big scary tracebacks in the stdout which look like SQLalchemy incompatibilities - are these a recent issue? $ git clone $ cd galaxy $ cp config/galaxy.ini.sample

Re: [galaxy-dev] problems splitting

2015-02-24 Thread Peter Cock
On Tue, Feb 24, 2015 at 4:43 PM, Roberto Alonso CIPF ralo...@cipf.es wrote: Hello again, first of all thanks for your help, it is being very useful. What I have done up to now is to copy this method to the class Sequence def get_split_commands_sequential(is_compressed, input_name,

Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread Peter Cock
On Thu, Feb 26, 2015 at 2:43 PM, John Chilton jmchil...@gmail.com wrote: Also not need to escape $__tool_directory__ (so use $__tool_directory__ instead of \$__tool_directory__). -John If this was unclear, $VAR in the command XML fragment is taken to be a Python variable available within

Re: [galaxy-dev] Importing file via FTP can silently fail, [Errno ftp error] 550

2015-02-26 Thread Peter Cock
On Thu, Feb 26, 2015 at 2:24 PM, John Chilton jmchil...@gmail.com wrote: Yeah - that is unfortunate - I agree completely that the resulting datasets should be red. I have created a Trello card here: https://trello.com/c/A6LrdjUU -John Thanks John, Does the new Download from URL or upload

Re: [galaxy-dev] Importing file via FTP can silently fail, [Errno ftp error] 550

2015-02-26 Thread Peter Cock
On Thu, Feb 26, 2015 at 2:24 PM, John Chilton jmchil...@gmail.com wrote: Yeah - that is unfortunate - I agree completely that the resulting datasets should be red. I have created a Trello card here: https://trello.com/c/A6LrdjUU -John I just commented on the Trello issue - as John implied

Re: [galaxy-dev] Multiple-select checkbox parameters not using default values

2015-03-27 Thread Peter Cock
On Fri, Mar 27, 2015 at 6:14 PM, Aysam Guerler aysam.guer...@gmail.com wrote: A fix for this is on the way. Thanks - if it can be applied on top of 15.03 that would be a bonus. Peter ___ Please keep all replies on the list by using reply

Re: [galaxy-dev] test/base/twilltestcase.py - Converting local (test-data) bam to sam failed

2015-03-23 Thread Peter Cock
On Tue, Mar 3, 2015 at 9:55 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Jan 27, 2015 at 2:23 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I have a query about a failing tool test on the Tool Shed, where it seems Galaxy is trying to convert both the expected BAM output

Re: [galaxy-dev] Tests not being run on toolsheds?

2015-03-23 Thread Peter Cock
Hi Dave, Can you check for stalls on the following repositories please? They've not been tested for nearly two months: https://toolshed.g2.bx.psu.edu/view/peterjc/clinod Last tested 2015-01-29, Exception: Job in error state. https://toolshed.g2.bx.psu.edu/view/peterjc/blast2go Last tested

Re: [galaxy-dev] value_from_basic - KeyError: 'base_name', was: Tests not being run on toolsheds?

2015-04-02 Thread Peter Cock
On Mon, Mar 23, 2015 at 12:27 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Dave, Now that you've fixed some of the test back log, the bad news is this issue I reported last week appears to be a major regression affecting multiple tools on the Test Tool Shed: https://testtoolshed.g2

Re: [galaxy-dev] wrapper accepts fastqcssanger when it shouldn't

2015-04-02 Thread Peter Cock
On Thu, Apr 2, 2015 at 10:02 AM, Nikhil Joshi najo...@ucdavis.edu wrote: Hi all, So in my wrapper for my trimming tool, sickle, I only allow fastq, fastqsanger, fastqillumina, or fastqsolexa input data. However, if a fastqsanger file's datatype has been erroneously changed to fastqcssanger,

[galaxy-dev] README.rst missing on Tool Shed display?

2015-04-24 Thread Peter Cock
Hi all, I don't see tool README files on the main view of a repository any more. Is this a recent regression? e.g. https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools and https://testtoolshed.g2.bx.psu.edu/view/bgruening/deeptools should show the readme.rst file e.g.

[galaxy-dev] UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped

2015-04-29 Thread Peter Cock
Hi all, I think this is the second time I've have the following error on TravisCI (last time I reran a similar failure, and it worked). I've not yet re-run the test so that you can see the full error log: UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped

Re: [galaxy-dev] optional tool arguments

2015-04-29 Thread Peter Cock
Yes, for example: https://github.com/peterjc/pico_galaxy/blob/master/tools/seq_filter_by_id/seq_filter_by_id.xml Peter On Wed, Apr 29, 2015 at 8:23 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Ryan I guess you can work with filters, see:

Re: [galaxy-dev] new tool works correctly but galaxy thinks it failed

2015-04-28 Thread Peter Cock
You probably need to set the stdio tag, since due to a historical design choice by default any output on stderr is treated as an error. See: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Peter On Tue, Apr 28, 2015 at 4:41 PM, Ryan G ngsbioinformat...@gmail.com wrote: Hi - I

Re: [galaxy-dev] UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped

2015-04-29 Thread Peter Cock
good understanding of now. We've tried a few different ideas for fixing it, (obviously none of which have worked, yet), and I've been poking at a new fix this week. -Dannon On Wed, Apr 29, 2015 at 6:53 AM Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I think this is the second time

Re: [galaxy-dev] PR 149

2015-04-29 Thread Peter Cock
On Wed, Apr 29, 2015 at 4:40 PM, Roberto Alonso CIPF ralo...@cipf.es wrote: Ok, no problems ;) It is another PR, I think it is useful without the other PR, for example when you map with BWA. The last PR will be like the next step, I mean for example that you split a bam to do some calling or

Re: [galaxy-dev] planemo questions

2015-04-27 Thread Peter Cock
On Mon, Apr 27, 2015 at 5:23 PM, Christian Brenninkmeijer christian.brenninkmei...@manchester.ac.uk wrote: Hi All, If there is a separate planemo mailing list please point me there. Not that I am aware of, galaxy-dev seems fine. I have been planing with planemo and find it a great tools.

Re: [galaxy-dev] code tagset in tools

2015-04-29 Thread Peter Cock
On Wed, Apr 29, 2015 at 6:33 AM, Simon Gladman simon.glad...@unimelb.edu.au wrote: Hi dev, Now that the code tagset is deprecated, how do we replace that functionality. For example the get microbial data tool runs the script listed in the code tagset to load the list of available microbe data

Re: [galaxy-dev] bam split and gatk calling

2015-05-06 Thread Peter Cock
Hi Roberto, Given the way BAM indexing works, I see no reason to actually split the BAM file at all - it seems like wasted disk IO. Instead, can you split a BED file into sub-regions? This way each child GATK job would look at the full BAM file but only for a small region described in the split

Re: [galaxy-dev] bam split and gatk calling

2015-05-06 Thread Peter Cock
On Wed, May 6, 2015 at 11:33 AM, Roberto Alonso CIPF ralo...@cipf.es wrote: Hello, I agree, what you say fits perfectly for GATK, but as I wanted to create a more generic code I did it this way (also because I am a newbie in the galaxy code and I didn't know so well how to implement this ).

Re: [galaxy-dev] 'Boolean' parameter type misbehaves in tool tests if truevalue starts with hyphen?

2015-05-08 Thread Peter Cock
On Fri, May 8, 2015 at 3:05 PM, Peter Briggs peter.bri...@manchester.ac.uk wrote: Hello I'm currently writing tests for a tool and think I've found a situation where the behaviour of the boolean parameter type does not seem correct within the test environment. The tool defines the

Re: [galaxy-dev] trinity tool form not allowing None input for strand-specificity

2015-05-11 Thread Peter Cock
On Fri, May 8, 2015 at 6:55 PM, Nicola Soranzo nsora...@tiscali.it wrote: The problem is not in the Cheetah code, which does not get executed because of the validation error. I think this a Galaxy bug which tries to validate the parameter values but interprets the value None of the

Re: [galaxy-dev] Galaxy on CentOS?

2015-05-05 Thread Peter Cock
Hi Carlos, We're running Galaxy on CentOS 6.6, so that in itself shouldn't be a problem. Most of the effort was sorting out shared storage with the cluster, which in our case is managed with SGE (fairly commonly used with Galaxy). In reply to your thread last month David Trudgian said he was

Re: [galaxy-dev] simple example of composite data types

2015-05-18 Thread Peter Cock
On Mon, May 18, 2015 at 1:55 PM, Brian Haas bh...@broadinstitute.org wrote: Thanks, Peter! I've verified that I can get your code to work - bundling the composite files. I'll keep plugging away at my little example and see if I can figure out what's going awry. more later. Thx again!

Re: [galaxy-dev] simple example of composite data types

2015-05-18 Thread Peter Cock
Hi Brian, Your original email with attachments has made it to the list now, http://dev.list.galaxyproject.org/difficulty-creating-composite-data-type-tp4667193.html Title: difficulty creating composite data type Peter On Mon, May 18, 2015 at 2:25 PM, Brian Haas bh...@broadinstitute.org wrote:

Re: [galaxy-dev] simple example of composite data types

2015-05-18 Thread Peter Cock
On Sun, May 17, 2015 at 5:44 PM, Brian Haas bh...@broadinstitute.org wrote: Greetings. Does anyone per chance have a simple working example of using composite data types? I've gotten as far as I can with the galaxy documentation, and I can't seem to get the additional files bundled into an

Re: [galaxy-dev] Geting integer value from InputValueWrapper in plugin xml file

2015-04-16 Thread Peter Cock
On Thu, Apr 16, 2015 at 1:59 PM, Christian Brenninkmeijer christian.brenninkmei...@manchester.ac.uk wrote: Hi, I am a new galaxy developer playing with writing my first plugins In my plugin xml configaration file: I want to be able to increase the value of one parameter based on another

Re: [galaxy-dev] Escaped HTML show in import-workflow red message

2015-04-08 Thread Peter Cock
Marten has added this to an existing issue - over zealous over escaping due to a security fix: https://trello.com/c/oX6i51Mn/2298-back-off-over-escaping Thanks, Peter On Wed, Apr 8, 2015 at 5:13 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I just imported a workflow and noticed

[galaxy-dev] Tool Shed installs: coercing to Unicode: need string or buffer, NoneType found

2015-04-09 Thread Peter Cock
I just hit a problem installing package_bx_python_0_7 via the Admin GUI. Name: bx-python Version: 0.7.1 Type: package Status: Error Error: Error installing tool dependency bx-python version 0.7.1: coercing to Unicode: need string or buffer, NoneType found Name: galaxy-ops Version: 1.0.0 Type:

Re: [galaxy-dev] keep job output and scripts on failed tests

2015-06-12 Thread Peter Cock
Hi Ryan, Something very handy for tool developers running functional tests is if the environment variable GALAXY_TEST_NO_CLEANUP is set, run_tests.sh shouldn't remove the test output. This is great when debugging why a test is failing. Peter On Fri, Jun 12, 2015 at 4:29 PM, Ryan G

Re: [galaxy-dev] keep job output and scripts on failed tests

2015-06-12 Thread Peter Cock
. On Fri, Jun 12, 2015 at 12:03 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Ryan, Something very handy for tool developers running functional tests is if the environment variable GALAXY_TEST_NO_CLEANUP is set, run_tests.sh shouldn't remove the test output. This is great when debugging

[galaxy-dev] devteam/fastqc (current) vs iuc/fastqc (obsolete?)

2015-05-27 Thread Peter Cock
Hi all, Searching on the main Tool Shed for fastqc gives two conflicting tools, an older version from the IUC, and a newer version from the devteam. If no one objects, I would like to mark the older IUC entry as deprecated, and edit the description to refer to the more up to date devteam entry

Re: [galaxy-dev] Cosmetic Makeblastdb error promulgated through wrapper

2015-07-04 Thread Peter Cock
Hi Damion, The NCBI have a bug here - if it is just a warning, it shouldn't say Error. We had something similar before: Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any. In that case the NCBI fixed it, see

Re: [galaxy-dev] Cosmetic Makeblastdb error promulgated through wrapper

2015-07-04 Thread Peter Cock
On Sat, Jul 4, 2015 at 5:09 PM, Dooley, Damion damion.doo...@bccdc.ca wrote: Sure I could probably step up to the plate on that one. I haven't reported it to NCBI - it didn't twig that this was an exit code 0 . I'll sneak it into BOSC codefest maybe! d. What is the error code? It might

Re: [galaxy-dev] Parallelism using metadata

2015-07-06 Thread Peter Cock
Hello all, Marco, Jon and I are going to try to get together during GCC2015 for a BOF (a Birds of a Feather informal meeting) to talk about Galaxy parallelisation (and collections). We've not yet picked a time, but details should be on the wiki shortly...

Re: [galaxy-dev] samtools index tool

2015-05-22 Thread Peter Cock
Galaxy itself will call samtools index on BAM files, so they should be there on disk already, See for example: https://github.com/peterjc/pico_galaxy/blob/master/tools/samtools_idxstats/samtools_idxstats.xml

[galaxy-dev] Tool installation problems within main Tool Shed test framework?

2015-05-26 Thread Peter Cock
Hi all, Looking at https://toolshed.g2.bx.psu.edu/ logged in a peterjc, the Repositories I Can Change / Latest revision: installation errors listing ought to be empty, but is very long (perhaps all my tools?). The individual tools show things like:

Re: [galaxy-dev] Adding BioPython as a dependency to Galaxy

2015-05-20 Thread Peter Cock
On Wed, May 20, 2015 at 3:39 PM, Eric Rasche e...@tamu.edu wrote: Howdy Devs, I'd like to see BioPython added as an egg. I mentioned this on IRC, but it sort of fell off. A couple of users spoke positively about having it as a dependency. Do any of the devs have further opinions on this?

Re: [galaxy-dev] Failure when preparing job on blastp

2015-07-21 Thread Peter Cock
Hi Peter v H, Which version of Galaxy are you running? Which version of ncbi_blast_tools are you running? (ideally down to the ToolShed revision) My guess is that since this used to be .extra_files_path perhaps your Galaxy is too old for .files_path to work?

Re: [galaxy-dev] Failure when preparing job on blastp

2015-07-21 Thread Peter Cock
no, its not an old Galaxy. On 21 July 2015 at 17:37, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Peter v H, Which version of Galaxy are you running? Which version of ncbi_blast_tools are you running? (ideally down to the ToolShed revision) My guess is that since this used

Re: [galaxy-dev] Failure when preparing job on blastp

2015-07-21 Thread Peter Cock
, Peter van Heusden p...@sanbi.ac.za wrote: Previous revision of ncbi_blast_plus works like a charm, thanks. On 21 July 2015 at 19:57, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks Peter, Yes, you are using the latest release published to the Tool Shed, aka v0.1.03 (internal changes

Re: [galaxy-dev] Switching history doesn't work with prefix

2015-07-23 Thread Peter Cock
Hello Ping, I can confirm this bug. I noticed this some time back when the new history was in beta, but neglected to explore what was wrong. Apologies. When looking at: http://our_server_name/galaxy/history/view_multiple Via Firefox I can see the switch button is triggering a URL like:

Re: [galaxy-dev] Object-Store, setting filetypes crashes Galaxy

2015-07-21 Thread Peter Cock
Hello all, This is resurrecting an old thread, but using $input.extra_files_path rather than $input.files_path explained an unfortunate regression in the BLAST+ wrappers reported earlier today: https://github.com/peterjc/galaxy_blast/issues/69 Thanks John for his detective work. Given

Re: [galaxy-dev] Spaces in GenomeSpaces file URLs from genomespace_importer tool

2015-10-21 Thread Peter Cock
ne of my failed jobs. > I also created a Trello bug submission. > > Regards, > > Marco > > On Wed, Oct 21, 2015 at 10:15 AM, Peter Cock <p.j.a.c...@googlemail.com> > wrote: >> >> Thanks Marco, >> >> OK, that seems to still be part of the Galaxy

[galaxy-dev] Deleting / deprecating an empty Tool Shed repository?

2015-10-22 Thread Peter Cock
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

Re: [galaxy-dev] search paths for custom tools

2015-10-26 Thread Peter Cock
The tools using Bioptyhon etc should declare a dependency, see e.g. https://github.com/biopython/galaxy_packages Use a repository_dependencies.xml file declaring this as a dependency, Also, in your tool XML file(s) you must include: biopython That should then trigger Galaxy to

Re: [galaxy-dev] search paths for custom tools

2015-10-26 Thread Peter Cock
/view/peterjc/align_back_trans Peter On Mon, Oct 26, 2015 at 4:16 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > The tools using Bioptyhon etc should declare a dependency, see e.g. > > https://github.com/biopython/galaxy_packages > > Use a repository_dependenci

Re: [galaxy-dev] search paths for custom tools

2015-10-26 Thread Peter Cock
On Mon, Oct 26, 2015 at 4:37 PM, Tony Schreiner wrote: > I take it the tool_dependencies.xml file goes in the same directory as the > custom tool xml files are. And as such applies to any of them in this > folder? > > Thanks > Tony They need to be in the same tar-ball

Re: [galaxy-dev] Tmhmm and signal P

2015-11-12 Thread Peter Cock
Hi Olivier, On Thu, Nov 12, 2015 at 1:03 PM, Olivier CLAUDE wrote: > Hi Björn! > > I do have signalP 3 , it's installed and on the path. Good. It is a shame that CBS use a proprietary license which forbids redistribution and packaging - otherwise I could have tried to

Re: [galaxy-dev] Tmhmm and signal P

2015-11-15 Thread Peter Cock
On Fri, Nov 13, 2015 at 11:08 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > On Fri, Nov 13, 2015 at 10:40 AM, Olivier CLAUDE <o.cla...@outlook.fr> wrote: >> >> Do anybody knows where i can find WolFPSORT? The >> website semms to be down for a while

Re: [galaxy-dev] Tmhmm and signal P

2015-11-12 Thread Peter Cock
On Thu, Nov 12, 2015 at 4:24 PM, Olivier CLAUDE wrote: > I followed the instuctions given by peter and signalp works with galaxy! > Thanks a lot! > Do I try the same for tmhmm2 and promoter2? > Thanks a lot again! > > Olivier Our notes from installing tmhmm2: TMHMM arrives

Re: [galaxy-dev] Bug when reading in tab seperated files

2015-11-17 Thread Peter Cock
Hi Christian, I think the "cvs" datatype sniffer should be fixed not to accept tab separated files, to me a clear false positive given Galaxy has a separate "tabular" format for "tsv" files. Also surprisingly the "tabular" datatype does not seem to have a sniff method at all:

Re: [galaxy-dev] Planemo 0.20.0 and xunit

2015-11-17 Thread Peter Cock
On Tue, Nov 17, 2015 at 2:48 PM, John Chilton wrote: > Thanks for the bug report. Somehow Galaxy isn't installing the > development wheels into the transient Galaxy's virtualenv, I've wiped > out my planemo caches and I can't reproduce this locally. Perhaps unrelated, but I

Re: [galaxy-dev] atlas 3.10 IUC error

2015-11-03 Thread Peter Cock
On Tue, Nov 3, 2015 at 6:16 PM, wrote: > Hi Nicola > > It is an i686. Is it a problem ? > > Cheers, > Olivier Currently only for 64bit Linux are pre-compiled binaries used:

Re: [galaxy-dev] blast2html

2015-10-08 Thread Peter Cock
Hi Juan, It does sounds like something in Galaxy's HTML security code could be to blame... Do you have any other HTML producing tools installed? It would be useful to see how their output behaves. e.g. The BLAST+ tools offer (very simple ugly) HTML output directly. Peter On Thu, Oct 8, 2015 at

Re: [galaxy-dev] Spaces in GenomeSpaces file URLs from genomespace_importer tool

2015-10-21 Thread Peter Cock
Hi Marco, I'd lay money on the the tool parameter sanitization done in Cheetah intended to avoid any command insertion into the shell command. This can be configured within the tool definition using the tag set:

Re: [galaxy-dev] Developing package wrappers

2015-10-20 Thread Peter Cock
On Tue, Oct 20, 2015 at 10:01 AM, Tiago Rodrigues Antao wrote: > Hi, > > I am afraid that I might be overlooking something obvious but... > > I am trying to add a few tools to the RAD-Seq portfolio of Galaxy. For > that effect I am designing a few package wrappers. My problem is

Re: [galaxy-dev] Tmhmm and signal P

2015-11-13 Thread Peter Cock
On Fri, Nov 13, 2015 at 10:40 AM, Olivier CLAUDE wrote: > Hello, > > This is working! For signlaP and promoter at least. > Good. > I still got this weird error with tmhmm ("no output from tmhmm") and I can't > figure what's wrong . > The message "no output from tmhmm" is

[galaxy-dev] Subtleties of and escaping dollar signs

2015-09-01 Thread Peter Cock
Hello all, I've just noticed that dollar signs for accessing environment variables must be escaped in the XML tag, but must not be escaped in the tag: https://github.com/peterjc/pico_galaxy/commit/4613a08139a3dfa07c3b0411ac8a91f55deabb74 I presume this is because is parsed as a Cheetah

Re: [galaxy-dev] Wiki documentation for tool_dependencies.xml file

2015-09-02 Thread Peter Cock
at 12:12 PM, Nicola Soranzo <nsora...@tiscali.it> wrote: > Hi Peter, > the page you are looking for is: > > https://wiki.galaxyproject.org/ToolDependenciesTagSets > > I think it should be better linked, I had to bookmark it! > > Cheers, > Nicola > > Il 02.09.2015 1

[galaxy-dev] Renaming pages on the Galaxy wiki

2015-09-02 Thread Peter Cock
Hi all, I just renamed a page on the wiki to fix a typo: https://wiki.galaxyproject.org/ToolsWitDependenciesInSameRepository now: https://wiki.galaxyproject.org/ToolsWithDependenciesInSameRepository I didn't see any option about setting up a redirection from the old URL (for pages linked to

[galaxy-dev] Wiki documentation for tool_dependencies.xml file

2015-09-02 Thread Peter Cock
Hi all, Is there a page on the wiki describing the tool_dependencies.xml file syntax? Searching finds pages with examples, e.g. https://wiki.galaxyproject.org/ToolsWithDependenciesInSameRepository https://wiki.galaxyproject.org/ComplexRepositoryDependencies What I am looking for is something

Re: [galaxy-dev] not sure what I can do about this...

2015-09-29 Thread Peter Cock
On Tue, Sep 29, 2015 at 1:12 PM, Fernandez Edgar wrote: > Hello Björn, > > Thank you for answering! > When I installed Prokka from the Galaxy ToolShed, all the dependencies were > installed too. > tbl2asn is one of those dependencies... > How would I replace it? > >

Re: [galaxy-dev] Creating R galaxy wrapper where a function checks file extension

2015-10-02 Thread Peter Cock
Creating symlinks with normal extensions is a common approach here where the Galaxy filenames won't work. Peter On Fri, Oct 2, 2015 at 10:57 AM, Martin Vickers wrote: > > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Hi all, > > I've been tasked with getting someone's R

Re: [galaxy-dev] Creating R galaxy wrapper where a function checks file extension

2015-10-02 Thread Peter Cock
in action? Is it done > in the xml wrapper somewhere or do I need to write a script that does this > and then call the Rscript? > > Cheers, > > Martin > > On 10/02/2015 11:13 AM, Peter Cock wrote: >> Creating symlinks with normal extensions is a common >> approa

  1   2   3   >