[galaxy-dev] bam_to_bigwig invalid syntax error
Dear experts, I've an issue with the bam_to_bigwig (brad-chapman) tool from the ToolShed. I've installed it using Conda to solve dependencies. When I run it on a bam file I get this error: Fatal error: Exit code 1 () File "/home/galaxy/shed_tools/ toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py", line 41 print "Have %i references" % len(sizes) ^ SyntaxError: invalid syntax I had a look in the job working directory. In the tool_script.sh the conda environment set is "$CONDA_DEFAULT_ENV" = "/export/job_work_dir/000/6/conda-env" (just in my case). Sourcing the conda environment, the python version is (/export/job_work_dir/000/6/conda-env) (.venv) [galaxy@vnode-0 6]$ python --version Python 3.6.2 Which is not compatible with the "print" code that we have in the bam_to_bigwig.py wrapper, at line 41. Any idea? Am I missing something? Best regards, Marco. ___ 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/
[galaxy-dev] Can't stop uwsgi processes with supervisod
Dear experts, I've a strange behaviour with uWSGI and supervisor. This is my settings in galaxy.ini file: [uwsgi] processes = 3 socket = 127.0.0.1:4001 stats = 127.0.0.1:9191 #socket = /var/log/galaxy/uwgi.sock pythonpath = /home/galaxy/galaxy/lib pythonhome = /home/galaxy/galaxy/.venv threads = 4 logto = /var/log/galaxy/uwsgi.log And this is my supervisord settings: [program:galaxy_web] command = /home/galaxy/galaxy/.venv/bin/uwsgi --ini-paste /home/galaxy/galaxy/config/galaxy.ini directory = /home/galaxy/galaxy umask = 022 autostart = true autorestart = true startsecs = 20 user= galaxy environment = VIRTUAL_ENV="/home/galaxy/galaxy/.venv",PATH="/home/galaxy/galaxy/.venv/bin:%(ENV_PATH)s",PYTHONHOME="/home/galaxy/galaxy/.venv" numprocs= 1 stopsignal = INT startretries= 15 The problem is that when I run galaxy with "supervisorctl start galaxy:" I've 4 galaxy process (ps -aux | grep uwsgi): galaxy 28795 13.0 1.0 1465320 177332 ? Sl 16:42 0:12 /home/galaxy/galaxy/.venv/bin/uwsgi --ini-paste /home/galaxy/galaxy/config/galaxy.ini galaxy 28950 1.2 1.0 1465320 170108 ? Sl 16:42 0:01 /home/galaxy/galaxy/.venv/bin/uwsgi --ini-paste /home/galaxy/galaxy/config/galaxy.ini galaxy 28951 1.1 1.0 1465320 170108 ? Sl 16:42 0:01 /home/galaxy/galaxy/.venv/bin/uwsgi --ini-paste /home/galaxy/galaxy/config/galaxy.ini galaxy 28953 0.0 1.0 1465320 166060 ? S16:42 0:00 /home/galaxy/galaxy/.venv/bin/uwsgi --ini-paste /home/galaxy/galaxy/config/galaxy.ini Once I did "supervisorctl stop galaxy:" I've: galaxy 28953 0.0 1.0 1465320 166060 ? S16:42 0:00 /home/galaxy/galaxy/.venv/bin/uwsgi --ini-paste /home/galaxy/galaxy/config/galaxy.ini there is still a uwsgi process (sometimes more, it depends on the uwsgi process number). I'm able to stop only those processes which have a "Sl" in the STAT column of "ps -aux | grep uwsgi": SInterruptible sleep (waiting for an event to complete) lis multi-threaded (using CLONE_THREAD, like NPTL pthreads do) (ps wiki) The problem is that I can't stop all the uwsgi processes, therefore I'm unable to restart galaxy, without killing all uwsgi processes. Thanks a lot, Marco. ___ 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] Python tool wrapper with multiple input and output files
Dear Marius and all,
thanks a lot for your answer, it is indeed very interesting.
I'm following this one
https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_two_paired.xml
to create an output list, starting from an input list.
The command section of my script_wrapper.xml looks like this:
Once I've run the tool in galaxy the job command line looks like:
python /home/galaxy/galaxy/tools/script-collection/script_wrapper.py -i
/home/galaxy/galaxy/database/files/000/dataset_269.dat -f
"/home/galaxy/galaxy/database/files/000/dataset_256.dat" -1
"/home/galaxy/galaxy/database/files/000/dataset_312.dat" -t
"${GALAXY_SLOTS:-4}"; script_wrapper.py -i
/home/galaxy/galaxy/database/files/000/dataset_254.dat -f
"/home/galaxy/galaxy/database/files/000/dataset_256.dat" -1
"/home/galaxy/galaxy/database/files/000/dataset_313.dat" -t
"${GALAXY_SLOTS:-4}";
And the output looks fine only for the first command in the job comman
line, becasue "python" is called only at the first iteration of the for
cycle.
Is there a way to prevent this behaviour or some "best practices" ?
Thanks a lot,
Marco.
2016-06-07 14:05 GMT+02:00 Marius van den Beek <m.vandenb...@gmail.com>:
> Hi Marco,
>
> you've got an interesting use-case there.
> You may want to use either a dataset list (if you only supply rna_n.bam),
> or a paired dataset list (rna_n.bam and dna_n.bam).
> I would probably implement a conditional, where the user selects either a
> dataset list or a paired dataset list.
> The output would then be another collection of output files.
> Have a look at the test tool folder, and see if any of the tools named
> collection_*.xml fits what you would like to do
> https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools
> These two may be a good basis for what you want to achieve:
>
> https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_list.xml
> [this one creates an output collection]
>
> https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_two_paired.xml
> [this one has a conditional to either select a list or a paired list as
> input]
>
> Let us know if you need more help!
>
> Cheers,
> Marius
>
> On 7 June 2016 at 09:50, Marco Tangaro <ma.tang...@gmail.com> wrote:
>
>> Dear experts,
>> my name is Marco and I'm working to port our python tool to the Galaxy
>> framework.
>> The main script needs a rna.bam file as input, a reference fasta file,
>> both mandatory. Finally, you can add a dna.bam file, but this is optional.
>> Therefore an example command is:
>>
>> script.py -i rna.bam -f reference.fa -j dna.bam
>>
>> The outout is a tabular.
>> Again the -j dna.bam option is completely optional.
>> So quite soon it turned out that I had to use a python wrapper to parse
>> our script. Now the wrapper works fine.
>>
>>
>> The next step is to run the tool over multiple input file and we would
>> like to avoid to use a workflow.
>>
>> The idea is that to each input file corresponds an output file. The
>> reference is still the same.
>> For instance, we have:
>>
>> rna_1.bam + dna_1.bam -> output_1.txt
>> rna_2.bam + dna_2.bam -> output_2.txt
>> rna_3.bam + dna_3.bam -> output_3.txt
>> ...
>> and so on.
>>
>>
>> But I don't know the best strategy to give to my wrapper multiple input
>> files.
>> Moreover I have to be sure, when the dna_xyz.bam files are uploaded, that
>> they correspond to the right rna_xyz.bam file.
>>
>> I would like to have as output a page which is showing as results the
>> link to the single output files as suggested here.
>> https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
>> planning to integrate a javascript interface.
>>
>> I've browsed a lot, but on multiple input file the posts are old.
>> I'm using the last galaxy release (16_04).
>>
>> I'm quite new to the galaxy world...
>> Thanks a lot for your suggestions,
>> Marco
>>
>> ___
>> 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/
>>
>
>
___
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[galaxy-dev] Python tool wrapper with multiple input and output files
Dear experts, my name is Marco and I'm working to port our python tool to the Galaxy framework. The main script needs a rna.bam file as input, a reference fasta file, both mandatory. Finally, you can add a dna.bam file, but this is optional. Therefore an example command is: script.py -i rna.bam -f reference.fa -j dna.bam The outout is a tabular. Again the -j dna.bam option is completely optional. So quite soon it turned out that I had to use a python wrapper to parse our script. Now the wrapper works fine. The next step is to run the tool over multiple input file and we would like to avoid to use a workflow. The idea is that to each input file corresponds an output file. The reference is still the same. For instance, we have: rna_1.bam + dna_1.bam -> output_1.txt rna_2.bam + dna_2.bam -> output_2.txt rna_3.bam + dna_3.bam -> output_3.txt ... and so on. But I don't know the best strategy to give to my wrapper multiple input files. Moreover I have to be sure, when the dna_xyz.bam files are uploaded, that they correspond to the right rna_xyz.bam file. I would like to have as output a page which is showing as results the link to the single output files as suggested here. https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files planning to integrate a javascript interface. I've browsed a lot, but on multiple input file the posts are old. I'm using the last galaxy release (16_04). I'm quite new to the galaxy world... Thanks a lot for your suggestions, Marco ___ 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/
