Re: [galaxy-dev] samtools index tool
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 https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/samtools/samtools_idxstats/samtools_idxstats.xml These demonstrate some different ways to find the BAI file. Peter On Fri, May 22, 2015 at 3:16 AM, Eleanor Morgan e.mor...@curtin.edu.au wrote: Hi all, Excuse me for the newbie question. I am developing a local instance of galaxy to use primarily for teaching purposes. I would like to index bam files produced in galaxy in order to view them in IGV. I can’t seem to find the samtools index tool in the toolshed. I can run samtools on the command line and generate indexes, but can find no way to add this functionality to the tool panel so that I can do it in Galaxy. I also can’t find this functionality in the tool panel (under Samtools or BAM tools) on usegalaxy.org. Am I missing something? Do I need to write my own tool? Regards, Eleanor Eleanor Morgan Senior Scientific Officer | School of Biomedical Sciences | Faculty of Health Sciences Curtin University Tel| +61 8 9266 7516 Mob | +61 408 004 369 Fax| +61 8 9266 2342 Email | e.mor...@curtin.edu.au Web| biomed.curtin.edu.au Curtin University is a trademark of Curtin University of Technology. CRICOS Provider Code 00301J (WA), 02637B (NSW) ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] error executing test
Roberto -
Sorry for consistently taking so long to respond to these parallelism
inquires - you are doing awesome work but I am just constantly swamped
- I'll try to do more testing today.
I can confirm both of those tests fail - it has nothing to do with your setup.
compare_bam_as_sam was added here:
https://github.com/galaxyproject/galaxy/commit/a38bae5cca98177eacaa3cdbeb74d3722263f377
It looks like I added a failing test to demonstrate metadata
generation was broken - and I was going to follow up on it and never
did.
parallelism_bam_filter_reads only ever existed in my fork on github
right? I am not sure why it failed - but you had some clues and I was
going to try to follow up. Once it is working I will open a pull
request for it.
If you are working on tests that is great - but I would focus on the
tests that work as examples. Some relevant ones may be:
test/functional/tools/parallelism_optional.xml
test/functional/tools/parallelism.xml
test/functional/tools/metadata_bam.xml
test/functional/tools/metadata_bcf.xml
These can be executed one at a time with:
./run_tests.sh -framework -id tool_id
... where tool id is the id in the tool XML file (which for these
tools usually match the basename of the file without the .xml
extension).
Will try to get to the pull requests today.
Thanks a bunch for your patience.
-John
On Mon, May 11, 2015 at 6:51 AM, Roberto Alonso CIPF ralo...@cipf.es wrote:
Hello,
I am designing some test and I have a problem, it works under the Galaxy web
environment, but it doesn't work when I try to use it as a test case. Indeed
I am trying other tests and they fail as well.
My test ./run_tests.sh -framework -id parallelism_bam_filter_reads says the
next:
==
ERROR: filter reads ( parallelism_bam_filter_reads ) Test-1
--
Traceback (most recent call last):
File /home/ralonso/galaxy/test/functional/test_toolbox.py, line 268, in
test_tool
self.do_it( td )
File /home/ralonso/galaxy/test/functional/test_toolbox.py, line 55, in
do_it
raise e
RunToolException: Error creating a job for these tool inputs - {u'type':
u'error', u'data': {u'input': u'History does not include a dataset of the
required format / build'}}
And the other test ./run_tests.sh -framework -id compare_bam_as_sam
==
ERROR: compare_bam_as_sam ( compare_bam_as_sam ) Test-1
--
Traceback (most recent call last):
File /home/ralonso/galaxy/test/functional/test_toolbox.py, line 268, in
test_tool
self.do_it( td )
File /home/ralonso/galaxy/test/functional/test_toolbox.py, line 37, in
do_it
stage_data_in_history( galaxy_interactor, testdef.test_data(),
test_history, shed_tool_id )
File /home/ralonso/galaxy/test/base/interactor.py, line 38, in
stage_data_in_history
upload_wait()
File /home/ralonso/galaxy/test/base/interactor.py, line 279, in wait
while not self.__history_ready( history_id ):
File /home/ralonso/galaxy/test/base/interactor.py, line 297, in
__history_ready
return self._state_ready( state, error_msg=History in error state. )
File /home/ralonso/galaxy/test/base/interactor.py, line 356, in
_state_ready
raise Exception( error_msg )
Exception: History in error state.
begin captured logging
Besides than it tries to migrate the database each time I try a test case
and it takes too long. I have seen that you can use --db postgres but it
doesn't work, I think this option should be user with --dockerize (that is
not my case).
would you have any idea of what is going on?
Best regards
--
Roberto Alonso
Functional Genomics Unit
Bioinformatics and Genomics Department
Prince Felipe Research Center (CIPF)
C./Eduardo Primo Yúfera (Científic), nº 3
(junto Oceanografico)
46012 Valencia, Spain
Tel: +34 963289680 Ext. 1021
Fax: +34 963289574
E-Mail: ralo...@cipf.es
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Re: [galaxy-dev] galaxy-dev Digest, Vol 107, Issue 22
on the same server via apache) such that galaxy provides a URL that will enable read access to these files. From what I could gather, there's no straightforward way to get a stable URL from galaxy that points to the extra_files in the composite data set, such as getting links to a bunch of bam files and indexes placed there. Assigning each of the extra files as metadata items (ie. similar to a bam.bai file as a metadata file for a single bam file) could have been an option, but I couldn't get that to work. For now, since my Galaxy instance and my web app are running on the same machine with access to the same file system, I'll just have my web app read the files directly from the galaxy database directory via symlinks set up by my galaxy tool during the run. It's a clunky way of doing things but should suffice for now given my setup. If others have better solutions, I'm definitely interested in hearing them. many thanks, ~brian ___ 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/ -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas -- next part -- An HTML attachment was scrubbed... URL: https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20150521/16ecbc3e/attachment-0001.html -- Message: 4 Date: Fri, 22 May 2015 02:16:33 + From: Eleanor Morgan e.mor...@curtin.edu.au To: galaxy-dev@lists.galaxyproject.org galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] samtools index tool Message-ID: d184af28.13a6f%e.mor...@curtin.edu.au Content-Type: text/plain; charset=iso-8859-1 Hi all, Excuse me for the newbie question. I am developing a local instance of galaxy to use primarily for teaching purposes. I would like to index bam files produced in galaxy in order to view them in IGV. I can't seem to find the samtools index tool in the toolshed. I can run samtools on the command line and generate indexes, but can find no way to add this functionality to the tool panel so that I can do it in Galaxy. I also can't find this functionality in the tool panel (under Samtools or BAM tools) on usegalaxy.org. Am I missing something? Do I need to write my own tool? Regards, Eleanor Eleanor Morgan Senior Scientific Officer | School of Biomedical Sciences | Faculty of Health Sciences Curtin University Tel| +61 8 9266 7516 Mob | +61 408 004 369 Fax| +61 8 9266 2342 Email | e.mor...@curtin.edu.aumailto:e.mor...@curtin.edu.au Web| biomed.curtin.edu.au [cid:ED62B336-732F-4D99-ABF8-AFACA1E1C7E3] Curtin University is a trademark of Curtin University of Technology. CRICOS Provider Code 00301J (WA), 02637B (NSW) -- next part -- An HTML attachment was scrubbed... URL: https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20150522/26eb90de/attachment-0001.html -- next part -- A non-text attachment was scrubbed... Name: 91CCC686-9541-451E-B585-2948E3C297CD[43].png Type: image/png Size: 5216 bytes Desc: 91CCC686-9541-451E-B585-2948E3C297CD[43].png URL: https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20150522/26eb90de/attachment-0001.png -- Message: 5 Date: Fri, 22 May 2015 09:46:59 +0100 From: Peter Cock p.j.a.c...@googlemail.com To: Eleanor Morgan e.mor...@curtin.edu.au Cc: galaxy-dev@lists.galaxyproject.org galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] samtools index tool Message-ID: CAKVJ-_4J6wY=nw-xthv0tvqryeznrzyzpwjv5w7rzocq+da...@mail.gmail.com Content-Type: text/plain; charset=utf-8 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 https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/samtools/samtools_idxstats/samtools_idxstats.xml These demonstrate some different ways to find the BAI file. Peter On Fri, May 22, 2015 at 3:16 AM, Eleanor Morgan e.mor...@curtin.edu.au wrote: Hi all, Excuse me for the newbie question. I am developing a local instance of galaxy to use primarily for teaching purposes. I would like to index bam files produced in galaxy in order to view them in IGV. I can’t seem to find the samtools index tool in the toolshed. I can run samtools on the command line and generate indexes, but can find no way to add this functionality to the tool panel so that I can do it in Galaxy. I also
