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. <philipp.rath...@ibc.uni-stuttgart.de>
Sent: Friday 5th August 2016 16:26
To: Peter Cock <p.j.a.c...@googlemail.com>
Cc: Brad Chapman <chapm...@50mail.com>; 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

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 <p.j.a.c...@googlemail.com 
<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/ 
> <http://code.google.com/p/pysam/> )
> genomeCoverageBed - part of BedTools (http://code.google.com/p/bedtools/ 
> <http://code.google.com/p/bedtools/> )
> bedGraphToBigWig  - from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/ 
> <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.
<philipp.rath...@ibc.uni-stuttgart.de 
<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
>  
> <http://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
>  
> <http://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
>  
> <http://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
>  
> <http://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
>  
> <http://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
>  
> <http://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 refere

Re: [galaxy-dev] Infinite recursion on conda dependency manager

2016-06-20 Thread Rathert , Philipp , Dr . 
Hi Björn,



this is not working 



root@galaxy:/galaxy-central# export 
PATH=/galaxy-central/tool_deps/_conda/bin/:$PATH

root@galaxy:/galaxy-central# conda install -y -q conda=3.19.3

bash: conda: command not found



cheers,



Philipp



-Original message-
From: Björn Grüning <bjoern.gruen...@gmail.com>
Sent: Monday 20th June 2016 13:21
To: Rathert, Philipp, Dr. <philipp.rath...@ibc.uni-stuttgart.de>; 
galaxy-dev@lists.galaxyproject.org
Cc: Björn Grüning <bjoern.gruen...@gmail.com>
Subject: Re: [galaxy-dev] Infinite recursion on conda dependency manager


Hi Philipp,

you are inside of the Docker container?

Can you do a:

export PATH=/galaxy-central/tool_deps/_conda/bin/:$PATH
conda install -y -q conda=3.19.3

Ciao,
Bjoern


Am 20.06.2016 um 13:01 schrieb Rathert, Philipp, Dr.:
> Dear all,
> 
> 
> 
> 
> 
>  I am trying to install bowtie as a dependency for bismarck. however, I am 
> getting the error posted below.
> 
> 
> 
> Maybe somebody has an idea how to fix this.
> 
> 
> 
> 
> 
> Thanks in advance,
> 
> 
> 
> philipp
> 
> 
> 
> 
> 
> In file included from SeqAn-1.1/seqan/basic.h:64:0,
>  from SeqAn-1.1/seqan/sequence.h:27,
>  from SeqAn-1.1/seqan/index.h:27,
>  from ebwt_build.cpp:5:
> SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void 
> seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)’:
> SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>ˆ
> SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename 
> seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type 
> seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)’:
> SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>ˆ
> SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void 
> seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)’:
> SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
>ˆ
> In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>  from SeqAn-1.1/seqan/index.h:27,
>  from ebwt_build.cpp:5:
> SeqAn-1.1/seqan/sequence/lexical.h: In function ‘void 
> seqan::compare_(seqan::Lexical&, TLeft&, TRight&)’:
> SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value::Type TLeftValue;
>   ˆ
> In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>  from SeqAn-1.1/seqan/index.h:27,
>  from ebwt_build.cpp:5:
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, 
> seqan::Tag)’:
> SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
> ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, 
> seqan::Tag)’:
> SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
> ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, 
> seqan::Tag)’:
> SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
> ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, 
> seqan::Tag)’:
> SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘T

Re: [galaxy-dev] History is not up-to-date

2016-06-20 Thread Rathert , Philipp , Dr . 
Dear Nicola,



I am using the 16.04 release. did you implement changes in this one recently?



Cheers,



Philipp

-Original message-
From: Nicola Soranzo <nsora...@tiscali.it>
Sent: Monday 20th June 2016 12:16
To: Rathert, Philipp, Dr. <philipp.rath...@ibc.uni-stuttgart.de>; 'Carl 
Eberhard' <carlfeberh...@gmail.com>
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] History is not up-to-date

 
 Hi Philipp,
 this has been fixed in the mean time on the release_16.04 branch of Galaxy, see
 
 https://github.com/galaxyproject/galaxy/pull/2506
 
 Can you try to update your Galaxy server in the container and check if it's 
working?
 
 Cheers,
 Nicola
 
 
On 20/06/16 10:31, Rathert, Philipp, Dr. wrote:
 
 

Hi Carl,
 

 


 

 

it looks like the time is not correct. 

 


 

 

 System Time: 2016-06-20T09:30:00.038328386Z

 

 EventsListeners: 0

 

 Init SHA1: 

 

 Init Path: /usr/local/bin/docker

 

 Docker Root Dir: /mnt/sda1/var/lib/docker

 

Labels:

 

 provider=virtualbox

 


 

 

the clock on my mac says 11:25

 


 

 


 

 

Is there an easy way to fix this or do I need to run galaxy in a new 
container? I run the container with -privileged=true, so it should be possible 
but so far I didn't find how...

 


 

 

Thanks for your help.

 


 

 

Cheers,

 


 

 

Philipp 

 


 

 


 

 


 

 


 

 -Original message-
 From: Philipp Rathert <philipp.rath...@ibc.uni-stuttgart.de>
 Sent: Wednesday 15th June 2016 9:07
 To: 'Carl Eberhard' <carlfeberh...@gmail.com>
 Cc: galaxy-dev@lists.galaxyproject.org
 Subject: Re: [galaxy-dev] History is not up-to-date
 
 
 
 

HI Carl,

 

 
 

I am travelling these days but will check on Monday. 

 

 
 

Thanks in advance.

 

 
 

Cheers,

 

 
 

Philipp 

 

 
 

From: Carl Eberhard [mailto:carlfeberh...@gmail.com] 
 Sent: Tuesday, June 14, 2016 6:24 PM
 To: Rathert, Philipp, Dr. <philipp.rath...@ibc.uni-stuttgart.de>
 Cc: galaxy-dev@lists.galaxyproject.org
 Subject: Re: [galaxy-dev] History is not up-to-date

 

 
 
 

Hi, Phillip

 
 

 
 
 
 

Quick questions:

 
 
 

- is the time properly set on the computer where you've got Galaxy running in 
the browser?

 
 
 

- is the time in the docker container also correct?

 
 
 

 
 
 
 

From you terminal output it looks like the update time might be the issue and 
we can then take it from there. Thanks

 
 
 

 
 
 
 
 

 
 
 

On Tue, Jun 14, 2016 at 11:28 AM, Rathert, Philipp, Dr. 
<philipp.rath...@ibc.uni-stuttgart.de> wrote:

 
 

Dear All,

 

 
 

 
 

I have a problem with my histories. 

 

We are running the Docker galaxy stable version 16.04 and when I start a tool 
the history does not show that it is running. it is not specific for any tool 
but for all.

 

 
 

 
 

 
 

 
 


 

 
 

 
 

however, something is running in the back

 

 
 

129.69.102.30 - - [14/Jun/2016:12:57:21 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A16.601Z
 HTTP/1.1" 200 - "http://129.69.102.42/; "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: 271|app: 0|req: 74/163] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:21 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A16.601Z
 => generated 2511 bytes in 33 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 2)

 

129.69.102.30 - - [14/Jun/2016:12:57:25 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A20.635Z
 HTTP/1.1" 200 - "http://129.69.102.42/; "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: 271|app: 0|req: 75/164] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:25 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A20.635Z
 => generated 2511 bytes in 29 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 1)

 

129.69.102.30 - - [14/Jun/2016:12:57:29 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A24.673Z
 HTTP/1.1" 200 - "http://129.69.102.42/; "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: 271|app: 0|req: 76/165] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:29 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A24.673Z
 => generated 2112 bytes in 30 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 0)

 

129.69.102.30 - - [14/Jun/2016:12:57:33 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A28.711Z
 HTTP/1.1" 200 - "http://129.69.102.42/; "M

[galaxy-dev] History is not up-to-date

2016-06-14 Thread Rathert , Philipp , Dr . 
Dear All,





I have a problem with my histories. 

We are running the Docker galaxy stable version 16.04 and when I start a tool 
the history does not show that it is running. it is not specific for any tool 
but for all.














however, something is running in the back



129.69.102.30 - - [14/Jun/2016:12:57:21 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A16.601Z
 HTTP/1.1" 200 - "http://129.69.102.42/  " "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: 271|app: 0|req: 74/163] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:21 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A16.601Z
 => generated 2511 bytes in 33 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 2)

129.69.102.30 - - [14/Jun/2016:12:57:25 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A20.635Z
 HTTP/1.1" 200 - "http://129.69.102.42/  " "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: 271|app: 0|req: 75/164] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:25 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A20.635Z
 => generated 2511 bytes in 29 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 1)

129.69.102.30 - - [14/Jun/2016:12:57:29 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A24.673Z
 HTTP/1.1" 200 - "http://129.69.102.42/  " "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: 271|app: 0|req: 76/165] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:29 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A24.673Z
 => generated 2112 bytes in 30 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 0)

129.69.102.30 - - [14/Jun/2016:12:57:33 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A28.711Z
 HTTP/1.1" 200 - "http://129.69.102.42/  " "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: 272|app: 0|req: 90/166] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:33 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A28.711Z
 => generated 2112 bytes in 32 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 0)

129.69.102.30 - - [14/Jun/2016:12:57:37 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A32.749Z
 HTTP/1.1" 200 - "http://129.69.102.42/  " "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: 271|app: 0|req: 77/167] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:37 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A32.749Z
 => generated 2112 bytes in 27 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 3)

 





I am not sure how to fix this and I am happy for any suggestion.



Cheers,



Philipp

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Re: [galaxy-dev] cleanup datasets error

2016-06-14 Thread Rathert , Philipp , Dr . 
Hi Bjoern,



I edited the galaxy.ini directly and started the script. Unfortunately I get a 
different error:





Traceback (most recent call last):

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 544, in 

    main()

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 104, in main

    app = CleanupDatasetsApplication( config )

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 529, in __init__

    self.model = galaxy.model.mapping.init( config.file_path, 
config.database_connection, engine_options={}, create_tables=False, 
object_store=self.object_store )

  File "/galaxy-central/lib/galaxy/model/mapping.py", line 2541, in init

    engine = build_engine( url, engine_options, database_query_profiling_proxy, 
trace_logger )

  File "/galaxy-central/lib/galaxy/model/orm/engine_factory.py", line 20, in 
build_engine

    engine = create_engine( url, proxy=proxy, **engine_options )

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/__init__.py",
 line 386, in create_engine

    return strategy.create(*args, **kwargs)

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py",
 line 75, in create

    dbapi = dialect_cls.dbapi(**dbapi_args)

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py",
 line 579, in dbapi

    import psycopg2

ImportError: No module named psycopg2



Can I install the python-psycopq2 module via apt-get in the container and would 
this help to fix thee issue?



Cheers,



Philipp



-Original message-
From: Rathert, Philipp, Dr. <philipp.rath...@ibc.uni-stuttgart.de>
Sent: Tuesday 14th June 2016 9:56
To: Bjoern Gruening <bjoern.gruen...@gmail.com>
Cc: galaxy-dev <galaxy-dev@lists.galaxyproject.org>
Subject: Re: [galaxy-dev] cleanup datasets error

Hi Bjoern,

This is wired. It worked before...
I will add this to the galaxy.ini in the config folder and try again.

Cheers,
Philipp

---Philipp on the road---

Am 14.06.2016 um 09:50 schrieb Bjoern Gruening <bjoern.gruen...@gmail.com 
<mailto:bjoern.gruen...@gmail.com> >:

 Hi,
 
 I don't think this will work with the script. This script reads the config 
file you specify config/galaxy.ini. And hence it needs to be added in this 
file, not via -e variables.
 This is probably something we should improve.
 
 Ciao,
 Bjoern
 
 
 > cleanup datasets error
 > 
 > HI Björn,
 > 
 > 
 > 
 > I have added these to the galaxy.ini via the docker specific e-
 > variables during startup of the container.
 > 
 > 
 > 
 > How can I check if they are broken?
 > 
 > 
 > 
 > Cheers,
 > 
 > 
 > 
 > Philipp
 > 
 > 
 > 
 > *From:*Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] *Sent:*
 > Tuesday, June 14, 2016 9:30 AM *To:* Rathert, Philipp, Dr.
 > <philipp.rath...@ibc.uni-stuttgart.de>; galaxy-dev
 > <galaxy-dev@lists.galaxyproject.org> *Subject:* Re: [galaxy-dev]
 > cleanup datasets error
 > 
 > 
 > 
 > Hi Philipp,
 > 
 > have you followed this from the readme?
 > 
 > 
 > Note that if you would like to run any of the cleanup scripts
 ><https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets>,
 > you will need to add the following to
 > |/export/galaxy-central/config/galaxy.ini|:
 > 
 > |database_connection =
 > postgresql://galaxy:galaxy@localhost:5432/galaxy| |file_path =
 > /export/galaxy-central/database/files|
 > 
 > Or is this broken? Cheers, Bjoern
 > 
 > On 14.06.2016 09:21, Rathert, Philipp, Dr. wrote:
 > 
 > Dear all,
 > 
 > 
 > 
 > when I want to start the cleanup datasets script I get the following
 > error.
 > 
 > 
 > 
 > (.venv)root@galaxy:/galaxy-central# python
 > /galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py
 > config/galaxy.ini -d -10 -1
 > 
 > Traceback (most recent call last):
 > 
 > File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
 > line 544, in 
 > 
 > main()
 > 
 > File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
 > line 99, in main
 > 
 > for key, value in config_parser.items( "app:main" ):
 > 
 > File "/usr/lib/python2.7/ConfigParser.py", line 642, in items
 > 
 > raise NoSectionError(section)
 > 
 > ConfigParser.NoSectionError: No section: 'app:main'
 > 
 > 
 > 
 > 
 > 
 > We are using the docker galaxy stable 16.04 version. Before this
 > script always worked without producing any error.
 > 
 > 
 > 
 > It would be great if anybody has an idea how to fix this...
 > 
 > 
 > 
 > Thank you very much in advance.
 > 
 > 
 &g

[galaxy-dev] cleanup datasets error

2016-06-14 Thread Rathert , Philipp , Dr . 
Dear all,



when I want to start the cleanup datasets script I get the following error.



(.venv)root@galaxy:/galaxy-central# python 
/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini 
-d -10 -1

Traceback (most recent call last):

  File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", line 
544, in 

    main()

  File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", line 99, 
in main

    for key, value in config_parser.items( "app:main" ):

  File "/usr/lib/python2.7/ConfigParser.py", line 642, in items

    raise NoSectionError(section)

ConfigParser.NoSectionError: No section: 'app:main'






We are using the docker galaxy stable 16.04 version. Before this script always 
worked without producing any error. 



It would be great if anybody has an idea how to fix this...



Thank you very much in advance.



Cheers,



Philipp 





-Original message-
From: Marius van den Beek 
Sent: Tuesday 7th June 2016 14:06
To: Marco Tangaro 
Cc: galaxy-dev 
Subject: Re: [galaxy-dev] Python tool wrapper with multiple input and 
outputfiles


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  > 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

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Re: [galaxy-dev] perl version 5.18.1 repository error

2016-03-24 Thread Rathert , Philipp , Dr . 
Dear Nicola,



now it looks like package_gnu_coreutils_8_22

is generating an error





gnu_coreutils 
<http://129.69.102.42/admin_toolshed/manage_repository_tool_dependencies?repository_id=e4c0e60daf76dabboperation=browsetool_dependency_ids=e96c6ce43a3d239a>
8.22package Error   Shutting down process id 23231 because it generated 
no output for the defined timeout period of 3600.0 seconds.







I didn't find anything an this error on the web and I am not sure how I can fix 
this...




cheers,



philipp 

-Original message-
From: Nicola Soranzo <nsora...@tiscali.it>
Sent: Wednesday 23rd March 2016 12:49
To: Rathert, Philipp, Dr. <philipp.rath...@ibc.uni-stuttgart.de>; 
galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] perl version 5.18.1 repository error

 Hi Philipp,
 can you try to reinstall the tool dependency? Go to the Admin interface, 
"Manage installed tools", click on the "package_perl_xml_parser_expat_2_41", 
then from the "Repository Actions" menu select "Manage tool dependencies", 
select the dependency in error and "Uninstall", then select it again and 
"Install" it.

 Cheers,
 Nicola

On 23/03/16 08:06, Rathert, Philipp, Dr. wrote:
Dear all,


 

i am trying to install  tool (meme-fimo) which needs 
package_perl_xml_parser_expat_2_41 that has a pearl 5.18.1 dependency.


 

however, although the tool installs just fine it shows that 
package_perl_xml_parser_expat_2_41 has missing dependencies:


 

Tool shed repository:package_perl_xml_parser_expat_2_41 
Tool shed repository changeset revision:1ce3818a8eb9 
Tool dependency status:Error 
Tool dependency installation error:Error installing tool dependency perl 
version 5.18.1: Unable to locate the repository directory for revision 
d905bb415eca of installed repository package_perl_5_18 owned by iuc. 
Tool dependency installation 
directory:././tool_deps/perl/5.18.1/iuc/package_perl_xml_parser_expat_2_41/1ce3818a8eb9

Is this an error of my local instance or is the revision missing on the 
toolshed?

Thank you very much for your help.

Cheers,

philipp 


 




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[galaxy-dev] perl version 5.18.1 repository error

2016-03-23 Thread Rathert , Philipp , Dr . 
Dear all,



i am trying to install  tool (meme-fimo) which needs 
package_perl_xml_parser_expat_2_41 that has a pearl 5.18.1 dependency.



however, although the tool installs just fine it shows that 
package_perl_xml_parser_expat_2_41 has missing dependencies:



Tool shed repository:package_perl_xml_parser_expat_2_41
 Tool shed repository changeset revision:1ce3818a8eb9
 Tool dependency status:Error
 Tool dependency installation error:Error installing tool dependency perl 
version 5.18.1: Unable to locate the repository directory for revision 
d905bb415eca of installed repository package_perl_5_18 owned by iuc.
 Tool dependency installation 
directory:././tool_deps/perl/5.18.1/iuc/package_perl_xml_parser_expat_2_41/1ce3818a8eb9

Is this an error of my local instance or is the revision missing on the 
toolshed?

Thank you very much for your help.

Cheers,

philipp 



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Re: [galaxy-dev] shed_tool_conf.xml

2016-03-22 Thread Rathert , Philipp , Dr . 
Hi Peter,



thx for the hint. Xcode was very helpful and I could localize the error.



However, this couldn't tell me why my label ids didn't work.

how do I implement those. Does this need a delimiter at the end like the 
sections?








Cheers,



Philipp

-Original message-
From: Peter Cock <p.j.a.c...@googlemail.com>
Sent: Tuesday 22nd March 2016 12:56
To: Rathert, Philipp, Dr. <philipp.rath...@ibc.uni-stuttgart.de>
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] shed_tool_conf.xml


I would try validating the broken XML file (e.g. using an online tool,
or an XML aware editor). That might be enough to find the error and
fix it by hand.

I don't know if there is a clever way to regenerate the file instead...

Peter


On Tue, Mar 22, 2016 at 11:49 AM, Rathert, Philipp, Dr.
<philipp.rath...@ibc.uni-stuttgart.de> wrote:
> Dear all,
>
>
> I think I made a really stupid mistake. I edited the shed_tool_con.xml file
> to change the order and section of tools.
>
>
> Doing this I might have introduced an error I cannot locate. However (now
> comes the stupidity), I didn't save the old version of the
> shed_tool_conf.xml file...
>
>
> Is there a way to fix this or do I have to reinstall all tools again?
>
>
> Thank you for your help.
>
>
> cheers,
>
>
> Philipp
>
>
> ___
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>
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[galaxy-dev] shed_tool_conf.xml

2016-03-22 Thread Rathert , Philipp , Dr . 
Dear all,



I think I made a really stupid mistake. I edited the shed_tool_con.xml file to 
change the order and section of tools.



Doing this I might have introduced an error I cannot locate. However (now comes 
the stupidity), I didn't save the old version of the shed_tool_conf.xml file...



Is there a way to fix this or do I have to reinstall all tools again?



Thank you for your help.



cheers,



Philipp 

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[galaxy-dev] Tool-install error with yaml file

2016-03-15 Thread Rathert , Philipp , Dr . 
Dear all, 
I want to install a bunch of tools using the install-tools 
function. In my yaml file tool.yml i have specified the url if my docker 
instance wit the ip adress i use in the web browser and the api_key is admin

When i run install-tools tool.yml I get the error below and nothing happens.

I attached my tool.yml file in case the error comes from there.

Anybody has an idea whats wrong?

root@galaxy:/galaxy-central# install-tools tool.yml * Starting PostgreSQL 
9.3 database server [ OK ] starting Galaxy Activating virtualenv at .venv 
Ignoring indexes: https://pypi.python.org/simple 
/galaxy-central/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315:
 
SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name 
Indication) extension to TLS is not available on this platform. This may 
cause the server to present an incorrect TLS certificate, which can cause 
validation failures. For more information, see 
https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning. 
SNIMissingWarning 
/galaxy-central/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120:
 
InsecurePlatformWarning: A true SSLContext object is not available. This 
prevents urllib3 from configuring SSL appropriately and may cause certain 
SSL connections to fail. For more information, see 
https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
 
InsecurePlatformWarning Requirement already up-to-date: pip==8.0.2+gx2 in 
./.venv/lib/python2.7/site-packages Requirement already satisfied 
(use --upgrade to upgrade): bx-python==0.7.3 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) 
Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23 
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) 
Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) 
Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8 
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) 
Requirement already satisfied (use --upgrade to upgrade): mercurial==3.4.2 
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) 
Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) 
Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) 
Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) 
Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2 
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) 
Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) 
Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) 
Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) 
Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) 
Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) 
Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) 
Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) 
Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) 
Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) 
Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) 
Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) 
Requirement already satisfied (use --upgrade to upgrade): Markdown==2.6.3 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) 
Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) 
Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in

Re: [galaxy-dev] cleanup

2016-02-23 Thread Rathert , Philipp , Dr . 
Dear Nicola,



thanks it worked. 





cheers,



Philipp

-Original message-
From: Nicola Soranzo <nsora...@tiscali.it>
Sent: Tuesday 23rd February 2016 20:35
To: Rathert, Philipp, Dr. <philipp.rath...@ibc.uni-stuttgart.de>; 
galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] cleanup

 
 Hi Philipp,
 please alway reply to the mailing list.
 
 I'm not using Docker, but if Galaxy is in the /galaxy-central/ directory and 
its version is 16.01, then:
 
 $ cd /galaxy-central/
 $ . .venv/bin/activate
 
$ python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d -30 
-1
 $ deactivate
 
 The command ". .venv/bin/activate" will activate the virtualenv installed in 
/galaxy-central/.venv/ , "deactivate" will deactivate it.
 
 Cheers,
 Nicola
 
 On 23/02/16 19:14, Rathert, Philipp, Dr. wrote:
 
 
Hi Nicola,
 
Could you be a bit more specific?
 
I guess i activate this in the specific container but how exactly?
 

 
 
Thanks a lot for your help.
 

 
 

 
 
Cheers,
 

 
 
Philipp
 ---Philipp on the road---
 

 Am 23.02.2016 um 16:20 schrieb Nicola Soranzo <nsora...@tiscali.it>:
 
 
 
 

 Hi Philipp,
 if you are using Galaxy release 16.01, you should load the virtualenv
 before running the cleanup script, e.g.:
 
 $ cd GALAXY_HOME
 $ . .venv/bin/activate
 $ python scripts/cleanup_datasets/cleanup_datasets.py ...
 
 Cheers,
 Nicola
 
 On 23/02/16 15:07, Hans-Rudolf Hotz wrote:
 > Hi Philipp
 >
 >
 > point 1 : that's as expected - good.
 >
 > point 2 : looks like a docker specific issue? Maybe Bjoern can jump in?
 >
 >
 > Hans-Rudolf
 >
 >
 >
 >
 > On 02/23/2016 12:17 PM, Rathert, Philipp, Dr. wrote:
 >> Dear Hans-Rudolf,
 >>
 >> thanks a lot for your help.
 >>
 >> I did as you suggested:
 >>
 >> 1. when I go into the scripts folder I get the error message you
 >> guessed:
 >> root@galaxy:/galaxy-central/scripts# python
 >> cleanup_datasets/cleanup_datasets.py
 >> /export/galaxy-central/config/galaxy.ini -d -30 -1
 >> Traceback (most recent call last):
 >> File "cleanup_datasets/cleanup_datasets.py", line 21, in 
 >>   import galaxy.config
 >> ImportError: No module named galaxy.config
 >>
 >>
 >> 2. from the root directory I recieve the following error message:
 >> root@galaxy:/galaxy-central# python
 >> scripts/cleanup_datasets/cleanup_datasets.py
 >> /export/galaxy-central/config/galaxy.ini -d -60 -1
 >> Traceback (most recent call last):
 >> File "scripts/cleanup_datasets/cleanup_datasets.py", line 21, in
 >> 
 >>   import galaxy.config
 >> File "/galaxy-central/lib/galaxy/config.py", line 21, in 
 >>   from galaxy.util.dbkeys import GenomeBuilds
 >> File "/galaxy-central/lib/galaxy/util/dbkeys.py", line 7, in
 >> 
 >>   from galaxy.util.object_wrapper import sanitize_lists_to_string
 >> File "/galaxy-central/lib/galaxy/util/object_wrapper.py", line
 >> 45, in
 >> 
 >>   from six.moves import UserDict
 >> ImportError: cannot import name UserDict
 >>
 >> Any idea what this means? I thought this should be automatically
 >> installed with python...
 >>
 >> Cheers,
 >>
 >> Philipp
 >>
 >>  -Original message-
 >>  *From:* Hans-Rudolf Hotz <h...@fmi.ch>
 >>  *Sent:* Monday 22nd February 2016 17:09
 >>  *To:* Rathert, Philipp, Dr. <philipp.rath...@ibc.uni-stuttgart.de>;
 >>  galaxy-dev@lists.galaxyproject.org
 >>  *Subject:* Re: [galaxy-dev] cleanup
 >>
 >>  Hi Philipp
 >>
 >>  > Since the new galaxy version, I am unable to perform a cleanup
 >> anymore.
 >>  >
 >>  >  From the galaxy root directory I want to start the script
 >>  > cleanup_datasets.py with the following line:
 >>  >
 >>  > $ python cleanup_datasets.py
 >> /export/galaxy-central/config/galaxy.ini -d
 >>  > -60 -1
 >>  >
 >>  > I get the error message:
 >>  >
 >>  > Can’t open file ‘cleanup_datasets.py’: no such file or directory.
 >>
 >>  Have you tried:
 >>
 >>  $ python scripts/cleanup_datasets/cleanup_datasets.py
 >>  /export/galaxy-central/config/galaxy.ini -d -60 -1
 >>
 >>  > But when I go into the folder in which the script is located
 >> it doesn’t
 >>  > work as well.
 >>
 >>  what is the error this time? Is it "ImportError: No module named
 >> galaxy"?
 >>
 >>
 >>  Regards, Hans-Rudolf
 >>
 >

[galaxy-dev] Docker and issue with shed_tool_conf.xml

2016-02-23 Thread Rathert , Philipp , Dr . 
Dear All,



I have a serious problem with installing new tools to our local 
Docker-galaxy-stable instance (latest version).



All tools seem to install without any issue from the tool shed. When I check 
under Manage installed tools they all show a green "installed" button.

However, the local tool shed is not updated anymore. none of the newly 
installed tools show up. It seems the shed_tool_conf.xml file is not updated.

the tools are all found in the folder shed_tools but not under tool-data, not 
sure if this means anything.




A work-around could be to manually enter these tools to the shed_tool_conf.xml 
file but to do this I wasn't able to find the guid for each tool. All other 
parameters are easy.

But this would be quite some effort and I am afraid that something is 
seriously wrong. 



It would be great to get your thoughts on this issue before I kill everything 
and start from scratch.



Thanks a lot.



Cheers,



Philipp 



PS: I am a wet lab scientist please be patient if I don't get everything 
immediately.


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Re: [galaxy-dev] NGS.plot script freeze

2016-02-14 Thread Rathert , Philipp , Dr . 
Hi Björn,
The browserpage freezes. And after some time it says: script freeze, debug or 
stop?

I do not manage to start the tool or even see the tool page.

Cheers,


Philipp

Am 13.02.2016 um 17:18 schrieb Björn Grüning  >:

Hi Phillipp,

what means the script freezes? Galaxy, or only the tool turns red?

Cheers,
Bjoern

Am 09.02.2016 um 12:58 schrieb Philipp Rathert:
> Dear All,
> 
> we are trying to use NGS-plot on our local docker-galaxy-stable instance.
> 
> The script freezes whenever we click on the tool.
> 
> Does anybody have an idea what is wrong and how to fix this?
> There is no error message or anything.
> Thank you very much.
> 
> Kind regards,
> 
> Philipp
> 
>  
> 
>  
> 
> 
> 
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> 
> 

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[galaxy-dev] CEAS error

2016-01-17 Thread Rathert , Philipp , Dr . 
Dear All,



We are running a local docker-galaxy-stable instance on a Mac OS X system. and 
observe a strange error:



CEAS
 Description:
 Revision:f411ce97a351

is not installing correctly.

After installing mysql-python in the container directly basically every package 
is installed:

Installed tool dependencies - click the name to browse the dependency 
installation directory
NameVersion TypeInstallation status
R 

  3.1.2   package Installed
ucsc_fetchChromSizes 

   1.0 package Installed
python_mysqldb 

 1.2.5   package Installed
bx_python 

  0.7.1   package Installed



Missing tool dependencies - click the name to install the missing dependency
NameVersion TypeInstallation status
cistrome_ceas 

1.0.2.d8c0751   package Error



cistrome_ceas 

1.0.2.d8c0751   package Error   The installation directory for this tool 
dependency had contents but the database had no record. The installation log 
may show this tool dependency to be correctly installed, but due to the missing 
database record it is now being set to Error.



A reinstall results in the same error on different dependencies and it looks 
like a random event.



Does anybody have an idea what could solve the issue?



I hope I provided enough information. In your answer please keep in mind I am a 
newcomer to all this and a wet lab scientist.



Thank you for your help.



Cheers,



philipp 

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