[galaxy-dev] protein ligand docking

2017-05-24 Thread Matthias Bernt 

Dear list,

I have recently evaluated the software for protein docking that is 
available in the toolshed. I could need some help / suggestions.


1. autodock_vina

The receptor of my example contains Au atoms which are not understood by 
autodock_vina. For autodock there is the possibility to add 
configuration for atoms:


http://autodock.scripps.edu/faqs-help/how-to/adding-new-atom-parameters-to-autodock

Does somebody know if this is also possible for autodock_vina in galaxy?

In my pdb file there are CONECT lines which cause autodock_vina to 
abort. If I remove them the program runs (when the Au atoms are also 
removed). So this is the smaller problem (Maybe this can be solved by 
extending openbabel).


2. rdock

Fails with a memory access failure

/gpfs1/data/galaxy_server/galaxy-dev/database/dependencies/_conda/envs/__rDock@2013.1/bin/rbcavity: 
Zeile 7: 104454 Speicherzugriffsfehler  (Speicherabzug geschrieben) 
"$RBT_ROOT/bin/$PROGNAME" "$@"


3. caddsuite_workflows + caddsuite_linux_x86_64 

The installation of the workflows works, but I do not see them in galaxy?

The installation of the other package fails with:

No information is available for the requested repository revision.
One or more of the following parameter values is likely invalid:
tool_shed_url: https://toolshed.g2.bx.psu.edu/
name: caddsuite_linux_x86_64
owner: marcel
changeset_revision: 026f5a483650

err_code: 48

4. BALL

I just tested one tool of the suite: ProteinProtonator. This fails with 
command not found.


Fatal error: Exit code 127 ()
/gpfs1/data/galaxy_server/galaxy-dev/jobs_dir/000/165/tool_script.sh: 
Zeile 9: ProteinProtonator: Kommando nicht gefunden.


Are there any suggestion on how to solve these problems or other options 
for docking with galaxy.


Cheers,
Matthias



--

---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
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Re: [galaxy-dev] python subprocess OSError when running bwa-mem

2017-05-24 Thread Hans-Rudolf Hotz 

Hi

run.sh

On 05/24/2017 10:51 AM, Georgios Nikolis wrote:

Hi Hans-Rudolf,
many thanks for pointing me to the right direction. samtools was
installed, it was indeed a problem with $PATH.
There are actually path setting scripts provides with the tools, also
for samtools, e.g.
database/dependencies/samtools/0.1.19/devteam/package_samtools_0_1_19/95d2c4aefb5f/env.sh
but it seems that they don't get executed automatically on server start.
I did it manually and bwa-mem runs now without errors.
We will have to see whether other tools besides samtools are affected.
Would you recommend that we put such path setting scripts into run.sh?


yes, at least for samtools, I guess this is currently the best option.

Regards, Hans-Rudolf



Best,
Georgios

On 05/22/2017 08:11 AM, Hans-Rudolf Hotz wrote:

Hi Georgios

I am just guessing here, but the error looks familiar:

Do you have samtools installed? and is it in $PATH?
(for a similar case, see: https://biostar.usegalaxy.org/p/19938/ )


Regards, Hans-Rudolf


On 05/19/2017 10:03 AM, Georgios Nikolis wrote:

Dear all,
we are currently working on a new local Galaxy instance (17.01) and we
encounter an error when running bwa-mem jobs. The jobs fail with a
python subprocess OSError triggered in the module
lib/galaxy/datatypes/binary.py
Here is the traceback:

Traceback (most recent call last):
   File "/opt/galaxy/galaxy/lib/galaxy/jobs/runners/__init__.py",
line 624, in finish_job
 job_state.job_wrapper.finish( stdout, stderr, exit_code )
   File "/opt/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 1350,
in finish
 dataset.datatype.set_meta( dataset, overwrite=False )
   File "/opt/galaxy/galaxy/lib/galaxy/datatypes/binary.py", line
391, in set_meta
 exit_code = subprocess.call( args=command, stderr=open(
stderr_name, 'wb' ))
   File "/usr/lib64/python2.7/subprocess.py", line 524, in call
 return Popen(*popenargs, **kwargs).wait()
   File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__
 errread, errwrite)
   File "/usr/lib64/python2.7/subprocess.py", line 1327, in
_execute_child
 raise child_exception
OSError: [Errno 2] No such file or directory

Has anyone seen this error before? Is there anything we can do to get
rid of it?

Thanks a lot!

Best,
Georgios


--
*Georgios Nikolis*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
IT Management Genomics Proteomics

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
phone: +49 6221 42-4659

g.niko...@dkfz.de 
www.dkfz.de 

logo 

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537





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Re: [galaxy-dev] python subprocess OSError when running bwa-mem

2017-05-24 Thread Georgios Nikolis 

  
  
Hi Hans-Rudolf,
many thanks for pointing me to the right direction. samtools was
installed, it was indeed a problem with $PATH. 
There are actually path setting scripts provides with the tools,
also for samtools, e.g.
database/dependencies/samtools/0.1.19/devteam/package_samtools_0_1_19/95d2c4aefb5f/env.sh
but it seems that they don't get executed automatically on server
start. I did it manually and bwa-mem runs now without errors.
We will have to see whether other tools besides samtools are
affected. Would you recommend that we put such path setting scripts
into run.sh?

Best,
Georgios

  
On 05/22/2017 08:11 AM, Hans-Rudolf
  Hotz wrote:

Hi
  Georgios
  
  
  I am just guessing here, but the error looks familiar:
  
  
  Do you have samtools installed? and is it in $PATH?
  
  (for a similar case, see: https://biostar.usegalaxy.org/p/19938/ )
  
  
  
  Regards, Hans-Rudolf
  
  
  
  On 05/19/2017 10:03 AM, Georgios Nikolis wrote:
  
  Dear all,

we are currently working on a new local Galaxy instance (17.01)
and we

encounter an error when running bwa-mem jobs. The jobs fail with
a

python subprocess OSError triggered in the module

lib/galaxy/datatypes/binary.py

Here is the traceback:

Traceback (most recent call last):
  
     File
  "/opt/galaxy/galaxy/lib/galaxy/jobs/runners/__init__.py", line
  624, in finish_job
  
   job_state.job_wrapper.finish( stdout, stderr, exit_code )
  
     File "/opt/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line
  1350, in finish
  
   dataset.datatype.set_meta( dataset, overwrite=False )
  
     File "/opt/galaxy/galaxy/lib/galaxy/datatypes/binary.py",
  line 391, in set_meta
  
   exit_code = subprocess.call( args=command, stderr=open(
  stderr_name, 'wb' ))
  
     File "/usr/lib64/python2.7/subprocess.py", line 524, in
  call
  
   return Popen(*popenargs, **kwargs).wait()
  
     File "/usr/lib64/python2.7/subprocess.py", line 711, in
  __init__
  
   errread, errwrite)
  
     File "/usr/lib64/python2.7/subprocess.py", line 1327, in
  _execute_child
  
   raise child_exception
  
  OSError: [Errno 2] No such file or directory
  

Has anyone seen this error before? Is there anything we can do
to get

rid of it?


Thanks a lot!


Best,

Georgios



--

*Georgios Nikolis*

Genomics and Proteomics Core Facility

High Throughput Sequencing (W190)

IT Management Genomics Proteomics


German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 580

69120 Heidelberg

Germany

phone: +49 6221 42-4659


g.niko...@dkfz.de 

www.dkfz.de 


logo 


Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef
Puchta

VAT-ID No.: DE143293537






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Re: [galaxy-dev] Decrease Galaxy polling of slurm?

2017-05-24 Thread Philip Blood 
Thanks Nate! I have no idea if this is actually having any impact, but
keeping admins happy is of utmost importance. :-)

Phil

On Wed, May 24, 2017 at 8:58 AM, Nate Coraor  wrote:

> Hi Phil,
>
> Unfortunately, there's no configurable for this. You can, however, modify
> the loop's sleep here:
>
> https://github.com/galaxyproject/galaxy/blob/
> d7a0fdfaa748ca427dda1cef74b81e253f1921d5/lib/galaxy/jobs/
> runners/__init__.py#L552
>
> Hope this helps,
> --nate
>
> On Wed, May 24, 2017 at 10:40 AM, Philip Blood  wrote:
>
>> An admin at our center noticed our Galaxy instance is polling slurm every
>> second and asked if the polling frequency can be decreased. Is there an
>> easy way to do this?
>>
>> Phil
>>
>> --
>> Philip D. Blood, Ph.D.
>> Senior Computational Scientist Voice: (412) 268-9329
>> Pittsburgh Supercomputing CenterFax: (412) 268-5832
>> Carnegie Mellon University   Email: bl...@psc.edu
>>
>> ___
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>>   http://galaxyproject.org/search/
>>
>
>


-- 
Philip D. Blood, Ph.D.
Senior Computational Scientist Voice: (412) 268-9329
Pittsburgh Supercomputing CenterFax: (412) 268-5832
Carnegie Mellon University   Email: bl...@psc.edu
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Re: [galaxy-dev] Decrease Galaxy polling of slurm?

2017-05-24 Thread Nate Coraor 
Hi Phil,

Unfortunately, there's no configurable for this. You can, however, modify
the loop's sleep here:

https://github.com/galaxyproject/galaxy/blob/d7a0fdfaa748ca427dda1cef74b81e253f1921d5/lib/galaxy/jobs/runners/__init__.py#L552

Hope this helps,
--nate

On Wed, May 24, 2017 at 10:40 AM, Philip Blood  wrote:

> An admin at our center noticed our Galaxy instance is polling slurm every
> second and asked if the polling frequency can be decreased. Is there an
> easy way to do this?
>
> Phil
>
> --
> Philip D. Blood, Ph.D.
> Senior Computational Scientist Voice: (412) 268-9329
> Pittsburgh Supercomputing CenterFax: (412) 268-5832
> Carnegie Mellon University   Email: bl...@psc.edu
>
> ___
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[galaxy-dev] Decrease Galaxy polling of slurm?

2017-05-24 Thread Philip Blood 
An admin at our center noticed our Galaxy instance is polling slurm every
second and asked if the polling frequency can be decreased. Is there an
easy way to do this?

Phil

-- 
Philip D. Blood, Ph.D.
Senior Computational Scientist Voice: (412) 268-9329
Pittsburgh Supercomputing CenterFax: (412) 268-5832
Carnegie Mellon University   Email: bl...@psc.edu
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[galaxy-dev] vcftools - errors running vcf-merge

2017-05-24 Thread Poole, Richard 
Hi all,

I am trying to run the vcf-merge tool, which depends on the vcftools 0.1.11 
package. I have this vcftools package and also the required tabix 0.2.6 both 
installed via the toolshed (tabix is set in the PATH of the Galaxy startup 
script). However, I keep getting gunzip error messages such as the following:

Log: tool progress
gunzip: error writing to output: Broken pipe
gunzip: 0.vcf.sorted.gz: uncompress failed
Using column name 'mutant' for 0.vcf.sorted.gz:mutant
Using column name 'sibling' for 0.vcf.sorted.gz:sibling
gunzip: error writing to output: Broken pipe
gunzip: 1.vcf.sorted.gz: uncompress failed
Using column name '1.vcf.sorted_mutant' for 1.vcf.sorted.gz:mutant
Using column name '1.vcf.sorted_sibling' for 1.vcf.sorted.gz:sibling

Does anyone have any idea how to solve this?

The command that the wrapper is generating is:

vcf-sort /Volumes/ngs/database/files/058/dataset_58073.dat > 0.vcf.sorted ; 
bgzip 0.vcf.sorted ; tabix -p vcf 0.vcf.sorted.gz ; vcf-sort 
/Volumes/ngs/database/files/058/dataset_58078.dat > 1.vcf.sorted ; bgzip 
1.vcf.sorted ; tabix -p vcf 1.vcf.sorted.gz ; vcf-merge 0.vcf.sorted.gz 
1.vcf.sorted.gz > /Volumes/ngs/database/files/058/dataset_58489.dat

Thanks,
Richard
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