Re: [galaxy-dev] Some plugin for digital normalization

2014-11-24 Thread Peter Cock
Hi Michael, I was just looking for the khmer Galaxy wrappers in order to try diginorm on some high coverage data, but they are not yet in the main ToolShed are they? I found this on the Test Tool Shed: https://testtoolshed.g2.bx.psu.edu/view/crusoe/khmer The last update date seems to match the

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

2014-11-27 Thread Peter Cock
, Peter On Wed, Nov 19, 2014 at 5:57 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks John, Fingers crossed we'll get some more detailed logs in a day or two :) Peter On Wed, Nov 19, 2014 at 5:48 PM, John Chilton jmchil...@gmail.com wrote: Hey Peter, Dave is out this week - so I have

[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] Nothing being tested on Test and main Tool Shed?

2014-12-10 Thread Peter Cock
On Thu, Nov 27, 2014 at 1:58 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Guys, I retitled this since the TestToolShed does seem to be running tests regularly again. However, I still have a fair number failing with the cryptic status Exception: History in error state. I guess

Re: [galaxy-dev] order of tools installed from toolshed

2014-12-10 Thread Peter Cock
this order to the Tools bar. Do I need an additional file to specify this order ? Best, Wolfgang On 12/10/2014 11:31 AM, Peter Cock wrote: Hi Wolfgang, You didn't include the name or a link to your Test Tool Shed packages. Are you talking about the suite_config.xml file? I'm not sure

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

2014-12-10 Thread Peter Cock
On Wed, Dec 10, 2014 at 2:03 PM, John Chilton jmchil...@gmail.com wrote: On Wed, Dec 10, 2014 at 5:46 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi guys, The good news is my list of failing tools has shrunk to the following, none of which seem to have been tested yet in December, stuck

Re: [galaxy-dev] order of tools installed from toolshed

2014-12-10 Thread Peter Cock
On Wed, Dec 10, 2014 at 2:08 PM, John Chilton jmchil...@gmail.com wrote: Peter - When you have previously asked about suite_config.xml I grepped around and I couldn't find any references to it, did some more greps just now and I still cannot. My best guess is that is not being used at all

Re: [galaxy-dev] When do tool tests run on main test toolsheds?

2014-12-11 Thread Peter Cock
Hi Peter B, Originally the tests were nightly, but due to the rising load this was dropped to every two or three days. As far as I know that is still the goal. Unfortunately the tool shed test system seems to be somewhat broken at the moment, see this thread starting last month:

Re: [galaxy-dev] join produces an import error

2014-12-11 Thread Peter Cock
On Wed, Dec 10, 2014 at 4:31 PM, Wang, Yu yu.w...@lrz.de wrote: Hi, I am testing Basic Protocol 1 on my local galaxy instance. But Join didn't work. What did I do wrong? I installed join from galaxy main tool shed, bx_python_0_7 was installed but with installation Status missing tool

[galaxy-dev] Functional tests using gzipped inputs have broken

2014-12-17 Thread Peter Cock
Hi all, Using gzipped input files in tool functional tests (which would be decompressed by the upload tool) used to work, e.g. https://travis-ci.org/peterjc/pico_galaxy/builds/42395911

Re: [galaxy-dev] Functional tests using gzipped inputs have broken

2014-12-17 Thread Peter Cock
/a74d32014b0512613042c2a44d0b946703a1fbcd The commit also includes a test case so hopefully this won't break again. -John On Wed, Dec 17, 2014 at 6:56 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, Using gzipped input files in tool functional tests (which would be decompressed

Re: [galaxy-dev] samtools installation problems

2014-12-31 Thread Peter Cock
Unfortunately the ToolShed dependency only provides samtools to individual Galaxy tools that declare a dependency on it. However, it allows multiple versions of samtools to be available to different (versions of) Galaxy tools. This does NOT provide a samtools on $PATH for Galaxy itself, and it

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

2015-02-04 Thread Peter Cock
On Fri, Jan 30, 2015 at 5:24 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Dannon, Nicola, This sounds very promising - I'll rerun the TravisCI job and we can expect it to work this time :) https://bitbucket.org/galaxy/galaxy-central/commits/3618b7a91e23096ecf7ce5842c1e16c749251a4d

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] parallesim

2015-02-05 Thread Peter Cock
Hi Roberto, Hans-Rudolf, I can confirm from personal testing that enabling the parallelism task-splitting in Galaxy does not work well with SQLite. This caused me problems with development and testing since my development Galaxy instance uses SQLite. As you found, testing with smaller splits is

Re: [galaxy-dev] parallesim

2015-02-06 Thread Peter Cock
On Fri, Feb 6, 2015 at 9:59 AM, Roberto Alonso CIPF ralo...@cipf.es wrote: Hello, Postgres did it perfectly, but as I would like to enable this option in my production servers I changed two configs in galaxy.ini: # This enables splitting of jobs into tasks, if specified by the particular

Re: [galaxy-dev] Manually adding new tools from toolshed

2015-01-15 Thread Peter Cock
On Thu, Jan 15, 2015 at 6:57 PM, Ryan G ngsbioinformat...@gmail.com wrote: Because of the way the infrastructure for my Galaxy instance is set up, I need to download and install tools from the toolshed manually. For most of the tools, this is pretty easy, however I'm now trying to add RSEM to

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

Re: [galaxy-dev] REMINDER: GalaxyAdmins Online Meetup on 19 February

2015-02-19 Thread Peter Cock
Thanks for the timely reminder Dave, Note that the John Hopkins system seems to use Adobe Connect which requires Flash Player 10.3 or above. I don't have that on my laptop, but my main excuse for not joining you all is I hadn't checked the start time based on my current location, and

[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] Tool Development DELLY

2015-01-09 Thread Peter Cock
On Thu, Jan 8, 2015 at 6:11 PM, Marco Albuquerque marcoalbuquerque@gmail.com wrote: Hello Galaxy, I'm currently working on adding some tools and am having an issue with DELLY. So, I am under the impression that BAM indexing happens automatically when a BAM is uploaded. However there is

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

2015-01-12 Thread Peter Cock
Hi Ryan, The problem isn't Galaxy stripping the extension, rather Galaxy is actually decompressing the file as part of the upload process. Unfortunately (and there is an open Trello enhancement request on this), Galaxy does not support sorting any of the defined datatypes in compressed form

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

Re: [galaxy-dev] fastq format recognition

2015-02-13 Thread Peter Cock
On Fri, Feb 13, 2015 at 12:08 PM, Michael Thon mike.t...@gmail.com wrote: I have a new galaxy installation on my server. I uploaded two fastq files and now I'm trying to run trimmomatic and fastqc. In both cases I am presented with a drop down list of fastq files to select from but the lists

Re: [galaxy-dev] problems splitting

2015-02-13 Thread Peter Cock
On Fri, Feb 13, 2015 at 11:38 AM, Nicola Soranzo nsora...@tiscali.it wrote: Il 13.02.2015 03:17 Peter Cock ha scritto: 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

Re: [galaxy-dev] How to test my functional tests?

2015-01-07 Thread Peter Cock
On Thu, Jan 8, 2015 at 3:27 AM, Jeltje van Baren jeltje.van.ba...@gmail.com wrote: Hi, I'm trying to find out what the best way is to see if my functional tests work as expected, and I'm also wondering when these tests are (supposed to be) run. Here are the details: Following instructions

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

2015-01-07 Thread Peter Cock
errors crop up. --Dave B. On 12/10/2014 09:19 AM, Peter Cock wrote: On Wed, Dec 10, 2014 at 2:03 PM, John Chilton jmchil...@gmail.com wrote: On Wed, Dec 10, 2014 at 5:46 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi guys, The good news is my list of failing tools has shrunk

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

2015-03-18 Thread Peter Cock
that blockage and a manual test run appears to have completed successfully, as should future automated test runs. As always, feel free to let us know if you encounter any additional inexplicable behavior. --Dave B. On 03/18/2015 07:00 AM, Peter Cock wrote: ... I can also confirm that the Test

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

2015-03-17 Thread Peter Cock
On Tue, Mar 17, 2015 at 1:20 PM, Peter Briggs peter.bri...@manchester.ac.uk wrote: Hello Apologies as this seems to be quite a frequent question (and I may have missed something) however: are the tool tests being executed on the main or test toolsheds at the moment? The most recent tests

[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] March 2015 Galaxy Release (v 15.03)

2015-03-17 Thread Peter Cock
Thanks Jen the whole Galaxy team. I'm slightly disappointed the four digit year lobby group (.mm) lost out to the yy.mm faction, but overall I'm very glad to see Galaxy finally has real version numbers :) Regards, Peter On Tue, Mar 17, 2015 at 2:37 PM, Jennifer Hillman-Jackson

Re: [galaxy-dev] Saving a Galaxy visualization (e.g. PNG or PDF) into the history / workflow

2015-03-13 Thread Peter Cock
On Fri, Mar 13, 2015 at 3:31 PM, Carl Eberhard carlfeberh...@gmail.com wrote: In short: Question: How can I save a static snapshot...? You can't yet. Question: If so, can I then ...recreate the pie chart? No, not yet. Overall, these are features that we definitely want and we are

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] Tests not being run on toolsheds?

2015-03-24 Thread Peter Cock
On Mon, Mar 23, 2015 at 9:54 AM, Peter Cock p.j.a.c...@googlemail.com wrote: 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

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

2015-03-23 Thread Peter Cock
On Mon, Mar 23, 2015 at 1:07 PM, John Chilton jmchil...@gmail.com wrote: It seems to be happening during upload - so it is not unsurprising that this error would affect multiple tools. I have checked out the exact revision registered in the tests and the uploads seem fine to me. You mean

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] Tool tests failing on Main Tool Shed with Exception: Job in error state.

2015-03-03 Thread Peter Cock
On Tue, Mar 3, 2015 at 9:51 AM, Peter Cock p.j.a.c...@googlemail.com wrote: 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

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

Re: [galaxy-dev] gatk tool config file

2015-03-02 Thread Peter Cock
On Mon, Mar 2, 2015 at 4:08 PM, Roberto Alonso CIPF ralo...@cipf.es wrote: Hello, I would like to add a very simple GATK wrapper to galaxy, but I am facing one problem. When you want to use UnifiedGenotyper tool, the extension of the bam file must be .bam, and when you upload something to

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

2015-02-27 Thread Peter Cock
On Fri, Feb 27, 2015 at 2:15 PM, John Chilton jmchil...@gmail.com wrote: Hey Peter, That database is pretty new (not yet in stable) - but you are tracking the master branch of galaxy on github in your tests (which is sortof like stable). You will want to either track the dev branch (so you

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

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

2015-02-27 Thread Peter Cock
On Thu, Feb 26, 2015 at 11:53 PM, Dooley, Damion damion.doo...@bccdc.ca wrote: Helop aI've been testing (using planemo) some tools scheduled for toolshed publication. My first test works, but Galaxy reports that the second one fails with: Parameter %s requires a value, but has no legal

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

2015-03-03 Thread Peter Cock
On Tue, Mar 3, 2015 at 5:32 PM, Dooley, Damion damion.doo...@bccdc.ca wrote: Ok, thanks Peter for the detailed feedback, change recommendations, and your work detailing all the NCBI Blast fields and quirks over time! The columns 25 and 26 stem from my predecessor's version of the code which

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

2015-03-03 Thread Peter Cock
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 and the tool's BAM output into SAM for comparison - but this fails. https

[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] custom java tools.xml : problem with classpath

2015-02-26 Thread Peter Cock
On Thu, Feb 26, 2015 at 1:35 PM, Pierre Lindenbaum pierre.lindenb...@univ-nantes.fr wrote: You'll need to white list the semi-colon which Galaxy has replaced as a security precaution (user free text can be exploited). See sanitizer here:

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

2015-02-26 Thread Peter Cock
On Thu, Feb 26, 2015 at 12:38 PM, Pierre Lindenbaum pierre.lindenb...@univ-nantes.fr wrote: Hi Peter, i wrote the tool_dependencies.xml ?xml version=1.0? tool_dependency package name=jvarkit version=1.0.0 install version=1.0.0 actions

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

2015-02-26 Thread Peter Cock
On Wed, Feb 25, 2015 at 5:33 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, Using either the legacy upload tool, or the new upload widget, the following FTP URL *appears* to load into Galaxy correctly giving a green history entry. However, on closer inspection it is an empty file

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] Planemo test fail if sys.error writen to

2015-05-14 Thread Peter Cock
Hi Christian, Can you show the complete example tool? In particular, what is the XML wrapper's stdio tag? By default Galaxy does treat anything on stderr as an error. See: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Peter On Thu, May 14, 2015 at 11:54 AM, Christian

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

  1   2   3   4   >