subject:"\[galaxy\-dev\] conversion issue"

Re: [galaxy-dev] conversion issue

2016-08-08 Thread Rathert , Philipp , Dr .

I tried to reinstall some tools, but I still get an error message:




Fatal error: Exit code 1 ()
bedtools: 
/galaxy-central/tool_deps/ucsc_tools/312/iuc/package_ucsc_tools_312/2d6bafd63401/lib/libstdc++.so.6:
 version `GLIBCXX_3.4.15' not found (required by bedtools)
needLargeMem: trying to allocate 0 bytes (limit: 1000)
Traceback (most recent call last):
  File 
"/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py",
 line 122, in 
main(*args, **kwargs)
  File 
"/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py",
 line 57, in main
convert_to_bigwig(temp_file, sizes, config, outfile)
  File 
"/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py",
 line 104, in convert_to_bigwig
subprocess.check_call(cl)
  File 
"/galaxy-central/tool_deps/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/subprocess.py",
 line 540, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['bedGraphToBigWig', '/tmp/tmpkiKe2V', 
'/export/galaxy-central/database/files/003/dataset_3153-sizes.txt', 
'/export/galaxy-central/database/files/003/dataset_3153.dat']' returned 
non-zero exit status 255





It seems Bedrolls requires 


GLIBCXX_3.4.15

Since I am using Galaxy-docker I am not sure how to get this installed...





Always grateful for help.



Cheers,



Philipp



-Original message-
From: Rathert, Philipp, Dr. 
Sent: Friday 5th August 2016 16:26
To: Peter Cock 
Cc: Brad Chapman ; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] conversion issue

Hi Peter,



it looks like samtools is not functional





==> /home/galaxy/logs/uwsgi.log <==

galaxy.tools DEBUG 2016-08-05 14:25:25,686 Validated and populated state for 
tool request (52.679 ms)

galaxy.tools.actions INFO 2016-08-05 14:25:25,754 Handled output named out for 
tool 
toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0 
(26.340 ms)

galaxy.tools.actions INFO 2016-08-05 14:25:25,767 Added output datasets to 
history (13.170 ms)

galaxy.tools.actions INFO 2016-08-05 14:25:25,793 Verified access to datasets 
for 
Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0]
 (11.785 ms)

galaxy.tools.actions INFO 2016-08-05 14:25:25,794 Setup for job 
Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0]
 complete, ready to flush (26.847 ms)

galaxy.tools.actions INFO 2016-08-05 14:25:25,841 Flushed transaction for job 
Job[id=2438,tool_id=toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0]
 (47.380 ms)

galaxy.tools.execute DEBUG 2016-08-05 14:25:25,842 Tool 
[toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0] 
created job [2438] (130.941 ms)

galaxy.tools.execute DEBUG 2016-08-05 14:25:25,851 Executed 1 job(s) for tool 
toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0 
request: (164.591 ms)

172.17.0.1 - - [05/Aug/2016:14:25:25 +] "POST /api/tools HTTP/1.1" 200 - 
"http://129.69.102.30:8080/root <http://129.69.102.30:8080/root> " "Mozilla/5.0 
(Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) 
Version/9.0.3 Safari/601.4.4"

[pid: 381|app: 0|req: 53/85] 172.17.0.1 () {52 vars in 973 bytes} [Fri Aug  5 
14:25:25 2016] POST /api/tools => generated 983 bytes in 256 msecs (HTTP/1.1 
200) 3 headers in 124 bytes (1 switches on core 0)

172.17.0.1 - - [05/Aug/2016:14:25:25 +] "GET 
/api/histories/b701da857886499b/contents?v=dev HTTP/1.1" 200 - 
"http://129.69.102.30:8080/root <http://129.69.102.30:8080/root> " "Mozilla/5.0 
(Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) 
Version/9.0.3 Safari/601.4.4"

[pid: 382|app: 0|req: 33/86] 172.17.0.1 () {46 vars in 921 bytes} [Fri Aug  5 
14:25:25 2016] GET /api/histories/b701da857886499b/contents?v=dev => generated 
125847 bytes in 127 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on 
core 2)



==> /home/galaxy/logs/handler0.log <==

galaxy.jobs DEBUG 2016-08-05 14:25:26,391 (2438) Working directory for job is: 
/export/galaxy-central/database/job_working_directory/002/2438

galaxy.jobs.handler DEBUG 2016-08-05 14:25:26,401 (2438) Dispatching to slurm 
runner

galaxy.jobs DEBUG 2016-08-05 14:25:26,436 (2438) Persisting job destination 
(destination id: slurm_cluster)

galaxy.jobs.runners DEBUG 2016-08-05 14:25:26,450 Job [2438] queued (48.081 ms)

galaxy.jobs.handler INFO 2016-08-05 14:25:26,457 (2438) Job dispatched

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,693 Building dependency shell 
command for depend

Re: [galaxy-dev] conversion issue

2016-08-05 Thread Rathert , Philipp , Dr .

rt/galaxy-central/database/files/003/dataset_3117.dat --split]

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,884 Building dependency shell 
command for dependency 'samtools'

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,884 Find dependency samtools 
version None

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,885 Resolver tool_shed_packages 
returned  
(isnull? True)

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,885 Resolver galaxy_packages 
returned  
(isnull? True)

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,886 Resolver galaxy_packages 
returned  
(isnull? True)

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,886 Resolver conda returned 
 (isnull? 
True)

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,887 Resolver conda returned 
 (isnull? 
True)

galaxy.tools.deps WARNING 2016-08-05 14:25:26,887 Failed to resolve dependency 
on 'samtools', ignoring

galaxy.jobs.runners DEBUG 2016-08-05 14:25:26,907 (2438) command is: mkdir -p 
working; cd working; 
/export/galaxy-central/database/job_working_directory/002/2438/tool_script.sh; 
return_code=$?; cd 
'/export/galaxy-central/database/job_working_directory/002/2438'; python 
"/export/galaxy-central/database/job_working_directory/002/2438/set_metadata_hmqtZc.py"
 "/export/galaxy-central/database/files/tmpBPe1aw" 
"/export/galaxy-central/database/job_working_directory/002/2438/working/galaxy.json"
 
"/export/galaxy-central/database/job_working_directory/002/2438/metadata_in_HistoryDatasetAssociation_3277_AUIB9T,/export/galaxy-central/database/job_working_directory/002/2438/metadata_kwds_HistoryDatasetAssociation_3277_5_v2O7,/export/galaxy-central/database/job_working_directory/002/2438/metadata_out_HistoryDatasetAssociation_3277_96qP8H,/export/galaxy-central/database/job_working_directory/002/2438/metadata_results_HistoryDatasetAssociation_3277_mCFIaX,/export/galaxy-central/database/files/003/dataset_3117.dat,/export/galaxy-central/database/job_working_directory/002/2438/metadata_override_HistoryDatasetAssociation_3277_Fi9GIQ"
 5242880; sh -c "exit $return_code"

galaxy.jobs.runners.drmaa DEBUG 2016-08-05 14:25:26,936 (2438) submitting file 
/export/galaxy-central/database/job_working_directory/002/2438/galaxy_2438.sh

galaxy.jobs.runners.drmaa DEBUG 2016-08-05 14:25:26,937 (2438) native 
specification is: --ntasks=1 --share

galaxy.jobs.runners.drmaa INFO 2016-08-05 14:25:26,938 (2438) queued as 7

galaxy.jobs DEBUG 2016-08-05 14:25:26,938 (2438) Persisting job destination 
(destination id: slurm_cluster)



==> /home/galaxy/logs/slurmctld.log <==

[2016-08-05T14:25:26.938] _slurm_rpc_submit_batch_job JobId=7 usec=251

[2016-08-05T14:25:26.941] sched: Allocate JobId=7 NodeList=5e2648045373 #CPUs=1



==> /home/galaxy/logs/slurmd.log <==

[2016-08-05T14:25:26.955] Launching batch job 7 for UID 1450



==> /home/galaxy/logs/handler0.log <==

galaxy.jobs.runners.drmaa DEBUG 2016-08-05 14:25:27,244 (2438/7) state change: 
job is running



==> /var/log/nginx/access.log <==

172.17.0.1 - admin [05/Aug/2016:14:25:30 +] "GET 
/api/histories/b701da857886499b/contents?v=dev&q=update_time-ge&qv=2016-08-05T14%3A25%3A26.000Z
 HTTP/1.1" 200 33 "http://129.69.102.30:8080/root 
<http://129.69.102.30:8080/root> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 
10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"



==> /home/galaxy/logs/slurmctld.log <==

[2016-08-05T14:25:30.946] completing job 7

[2016-08-05T14:25:30.947] sched: job_complete for JobId=7 successful, exit 
code=0



==> /home/galaxy/logs/slurmd.log <==

[2016-08-05T14:25:30.945] [7] sending REQUEST_COMPLETE_BATCH_SCRIPT, error:0

[2016-08-05T14:25:30.947] [7] done with job







I will check if anything is wrong on that side...



-Original message-
From: Peter Cock 
Sent: Friday 5th August 2016 16:15
To: Rathert, Philipp, Dr. 
Cc: galaxy-dev@lists.galaxyproject.org; Brad Chapman 
Subject: Re: [galaxy-dev] conversion issue


I think you will need to look at the Galaxy logs for some clues
about if the dependencies are being found or not. The simple
"hack" is to install them on the $PATH manually, which would
be the practical solution if this is urgent.

Peter

On Fri, Aug 5, 2016 at 3:09 PM, Rathert, Philipp, Dr.
 wrote:
> Yes I did.
> All tools are installed and I see no error message.
>
> Philipp

___
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] conversion issue

2016-08-05 Thread Peter Cock

I think you will need to look at the Galaxy logs for some clues
about if the dependencies are being found or not. The simple
"hack" is to install them on the $PATH manually, which would
be the practical solution if this is urgent.

Peter

On Fri, Aug 5, 2016 at 3:09 PM, Rathert, Philipp, Dr.
 wrote:
> Yes I did.
> All tools are installed and I see no error message.
>
> Philipp
___
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] conversion issue

2016-08-05 Thread Rathert , Philipp , Dr .

Yes I did.
All tools are installed and I see no error message.

Philipp

---Philipp on the road---

Am 05.08.2016 um 15:31 schrieb Peter Cock mailto:p.j.a.c...@googlemail.com> >:

Its sounds like bedGraphToBigWig has not been installed.

https://toolshed.g2.bx.psu.edu/view/brad-chapman/bam_to_bigwig/

The README says:

> Ensure the following command line tools are on the system path:
>
> pysam - Python interface to samtools (http://code.google.com/p/pysam/ 
>  )
> genomeCoverageBed - part of BedTools (http://code.google.com/p/bedtools/ 
>  )
> bedGraphToBigWig  - from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/ 
>  )

However, the tool does appear to declare the dependencies via
the Tool Shed mechanism - did you install them via the Tool Shed?

Peter

On Fri, Aug 5, 2016 at 2:23 PM, Rathert, Philipp, Dr.
mailto:philipp.rath...@ibc.uni-stuttgart.de> > wrote:
> Dear All,
>
>
> I get the following errors when I try to Convert BAM to BigWig
>
>
> Traceback (most recent call last):
>   File
> "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py
>  
> 
>  ",
> line 103, in 
> main(*args, **kwargs)
>   File
> "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py
>  
> 
>  ",
> line 48, in main
> convert_to_graph(bam_file, split, config, temp_handle)
>   File
> "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py
>  
> 
>  ",
> line 76, in convert_to_graph
> subprocess.check_call(cl, stdout=out_handle)
>   File "/usr/lib/python2.7/subprocess.py", line 535, in check_call
> retcode = call(*popenargs, **kwargs)
>   File "/usr/lib/python2.7/subprocess.py", line 522, in call
> return Popen(*popenargs, **kwargs).wait()
>   File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
> errread, errwrite)
>   File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
> raise child_exception
> OSError: [Errno 2] No such file or directory
>
> The tool produced the following additional output:
>
> Have 93 references
> Calculating coverage...
>
> or
>
> Fatal error: Exit code 1 ()
> bedtools:
> /galaxy-central/tool_deps/ucsc_tools/312/iuc/package_ucsc_tools_312/2d6bafd63401/lib/libstdc++.so.6:
> version `GLIBCXX_3.4.15' not found (required by bedtools)
> needLargeMem: trying to allocate 0 bytes (limit: 1000)
> Traceback (most recent call last):
>   File
> "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py
>  
> 
>  ",
> line 122, in 
> main(*args, **kwargs)
>   File
> "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py
>  
> 
>  ",
> line 57, in main
> convert_to_bigwig(temp_file, sizes, config, outfile)
>   File
> "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py
>  
> 
>  ",
> line 104, in convert_to_bigwig
> subprocess.check_call(cl)
>   File
> "/galaxy-central/tool_deps/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/subprocess.py",
> line 540, in check_call
> raise CalledProcessError(retcode, cmd)
> subprocess.CalledProcessError: Command '['bedGraphToBigWig',
> '/tmp/tmp2F67r6',
> '/export/galaxy-central/database/files/003/dataset_3116-sizes.txt',
> '/export/galaxy-central/database/files/003/dataset_3116.dat']' returned
> non-zero exit status 255
>
> The tool produced the following additional output:
>
> Have 93 references
> Calculating coverage...
> Converting 0 MB graph file to bigwig..
>
> depending what version of the tool i am using.
>
>
> Any idea what this can be?
>
>
> I am using the latest Docker-galaxy-stable version (16.04) but I think this
> is not related to docker. All tools are updated.
>
>
> Thank you very much for your help,
>
>
> Philipp
>
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and

Re: [galaxy-dev] conversion issue

2016-08-05 Thread Peter Cock

Its sounds like bedGraphToBigWig has not been installed.

https://toolshed.g2.bx.psu.edu/view/brad-chapman/bam_to_bigwig/

The README says:

> Ensure the following command line tools are on the system path:
>
> pysam - Python interface to samtools (http://code.google.com/p/pysam/)
> genomeCoverageBed - part of BedTools (http://code.google.com/p/bedtools/)
> bedGraphToBigWig  - from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)

However, the tool does appear to declare the dependencies via
the Tool Shed mechanism - did you install them via the Tool Shed?

Peter

On Fri, Aug 5, 2016 at 2:23 PM, Rathert, Philipp, Dr.
 wrote:
> Dear All,
>
>
> I get the following errors when I try to Convert BAM to BigWig
>
>
> Traceback (most recent call last):
>   File
> "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py",
> line 103, in 
> main(*args, **kwargs)
>   File
> "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py",
> line 48, in main
> convert_to_graph(bam_file, split, config, temp_handle)
>   File
> "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py",
> line 76, in convert_to_graph
> subprocess.check_call(cl, stdout=out_handle)
>   File "/usr/lib/python2.7/subprocess.py", line 535, in check_call
> retcode = call(*popenargs, **kwargs)
>   File "/usr/lib/python2.7/subprocess.py", line 522, in call
> return Popen(*popenargs, **kwargs).wait()
>   File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
> errread, errwrite)
>   File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
> raise child_exception
> OSError: [Errno 2] No such file or directory
>
> The tool produced the following additional output:
>
> Have 93 references
> Calculating coverage...
>
> or
>
> Fatal error: Exit code 1 ()
> bedtools:
> /galaxy-central/tool_deps/ucsc_tools/312/iuc/package_ucsc_tools_312/2d6bafd63401/lib/libstdc++.so.6:
> version `GLIBCXX_3.4.15' not found (required by bedtools)
> needLargeMem: trying to allocate 0 bytes (limit: 1000)
> Traceback (most recent call last):
>   File
> "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py",
> line 122, in 
> main(*args, **kwargs)
>   File
> "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py",
> line 57, in main
> convert_to_bigwig(temp_file, sizes, config, outfile)
>   File
> "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py",
> line 104, in convert_to_bigwig
> subprocess.check_call(cl)
>   File
> "/galaxy-central/tool_deps/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/subprocess.py",
> line 540, in check_call
> raise CalledProcessError(retcode, cmd)
> subprocess.CalledProcessError: Command '['bedGraphToBigWig',
> '/tmp/tmp2F67r6',
> '/export/galaxy-central/database/files/003/dataset_3116-sizes.txt',
> '/export/galaxy-central/database/files/003/dataset_3116.dat']' returned
> non-zero exit status 255
>
> The tool produced the following additional output:
>
> Have 93 references
> Calculating coverage...
> Converting 0 MB graph file to bigwig..
>
> depending what version of the tool i am using.
>
>
> Any idea what this can be?
>
>
> I am using the latest Docker-galaxy-stable version (16.04) but I think this
> is not related to docker. All tools are updated.
>
>
> Thank you very much for your help,
>
>
> Philipp
>
>
>
>
> ___
> 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/

[galaxy-dev] conversion issue

2016-08-05 Thread Rathert , Philipp , Dr .

Dear All,



I get the following errors when I try to Convert BAM to BigWig




Traceback (most recent call last):
  File 
"/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py",
 line 103, in 
main(*args, **kwargs)
  File 
"/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py",
 line 48, in main
convert_to_graph(bam_file, split, config, temp_handle)
  File 
"/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py",
 line 76, in convert_to_graph
subprocess.check_call(cl, stdout=out_handle)
  File "/usr/lib/python2.7/subprocess.py", line 535, in check_call
retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python2.7/subprocess.py", line 522, in call
return Popen(*popenargs, **kwargs).wait()
  File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
errread, errwrite)
  File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory


The tool produced the following additional output:


Have 93 references
Calculating coverage...

or 


Fatal error: Exit code 1 ()
bedtools: 
/galaxy-central/tool_deps/ucsc_tools/312/iuc/package_ucsc_tools_312/2d6bafd63401/lib/libstdc++.so.6:
 version `GLIBCXX_3.4.15' not found (required by bedtools)
needLargeMem: trying to allocate 0 bytes (limit: 1000)
Traceback (most recent call last):
  File 
"/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py",
 line 122, in 
main(*args, **kwargs)
  File 
"/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py",
 line 57, in main
convert_to_bigwig(temp_file, sizes, config, outfile)
  File 
"/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py",
 line 104, in convert_to_bigwig
subprocess.check_call(cl)
  File 
"/galaxy-central/tool_deps/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/subprocess.py",
 line 540, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['bedGraphToBigWig', '/tmp/tmp2F67r6', 
'/export/galaxy-central/database/files/003/dataset_3116-sizes.txt', 
'/export/galaxy-central/database/files/003/dataset_3116.dat']' returned 
non-zero exit status 255


The tool produced the following additional output:


Have 93 references
Calculating coverage...
Converting 0 MB graph file to bigwig..

depending what version of the tool i am using.



Any idea what this can be?



I am using the latest Docker-galaxy-stable version (16.04) but I think this is 
not related to docker. All tools are updated.



Thank you very much for your help,



Philipp





___
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] conversion issue

Re: [galaxy-dev] conversion issue

Re: [galaxy-dev] conversion issue

Re: [galaxy-dev] conversion issue

Re: [galaxy-dev] conversion issue

[galaxy-dev] conversion issue

6 matches

Site Navigation

Mail list logo

Footer information