Re: [galaxy-dev] Difficulty uploading BAM files

[Scott Szakonyi]

Hi Peter,

Thanks to you and all the other responders who were so helpful! This did
solve my problem right away.

Best regards,

Scott

On Fri, Feb 26, 2016 at 3:13 PM, Peter Cock 
wrote:

> Hi Scott,
>
> Galaxy itself requires samtools (to deal with BAM files), separately
> from any Tool Dependency within the tool calling framework.
>
> Right now there is no mechanism for datatype definitions to declare a
> dependency (e.g. on a binary like samtools, or a Python library).
>
> Probably samtools should be listed as a requirement on the wiki?
> https://wiki.galaxyproject.org/Admin/GetGalaxy
>
> Peter
>
> On Fri, Feb 26, 2016 at 5:49 PM, Scott Szakonyi
>  wrote:
> > Hi,
> >
> > I'm having trouble uploading BAM files in our development environment.
> Other
> > files types are uploading without issue. I'm testing with a small BAM
> file I
> > downloaded, and I'm able to successfully upload it on our production
> server
> > and usegalaxy.org. When I try to upload in the development environment,
> I
> > get the following error:
> >
> > Traceback (most recent call last):
> >   File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line
> > 431, in 
> > __main__()
> >   File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line
> > 420, in __main__
> > add_file( dataset, registry, json_file, output_path )
> >   File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line
> > 347, in add_file
> > if link_data_only == 'copy_files' and
> > datatype.dataset_content_needs_grooming( output_path ):
> >   File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py",
> line
> > 218, in dataset_content_needs_grooming
> > version = self._get_samtools_version()
> >   File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py",
> line
> > 179, in _get_samtools_version
> > raise Exception(message)
> > Exception: Attempting to use functionality requiring samtools, but it
> cannot
> > be located on Galaxy's PATH.
> >
> > I've checked my installed tools, and all the same Samtools packages are
> > successfully installed on the development environment as in production. I
> > don't see any missing dependencies or anything like that. At this point
> I'm
> > stumped. If anyone can offer some guidance on how to resolve this, I'd be
> > most appreciative.
> >
> > Best regards,
> >
> > --
> > Scott B. Szakonyi
> > Research Programmer
> >
> > Center for Research Computing
> > 107 Information Technology Center
> > Notre Dame, IN 46556
> > http://crc.nd.edu
> >
> > ___
> > 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/
>



-- 
Scott B. Szakonyi
Research Programmer

*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu
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Re: [galaxy-dev] Difficulty uploading BAM files

[Christian Brenninkmeijer]

It is a shame and a but surprising that unlike most other dependencies samtools 
can not come from an egg now wheel.

Christian

From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Marius van den Beek [m.vandenb...@gmail.com]
Sent: Friday, February 26, 2016 6:01 PM
To: Scott Szakonyi
Cc: Galaxy Dev Mailing List
Subject: Re: [galaxy-dev] Difficulty uploading BAM files

Hello Scott,

you do need a samtools binary on GALAXY's PATH.
This is not samtools installed from the toolshed.

Best,
Marius

On 26 February 2016 at 18:49, Scott Szakonyi 
> wrote:
Hi,

I'm having trouble uploading BAM files in our development environment. Other 
files types are uploading without issue. I'm testing with a small BAM file I 
downloaded, and I'm able to successfully upload it on our production server and 
usegalaxy.org. When I try to upload in the development 
environment, I get the following error:

Traceback (most recent call last):
  File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 431, 
in 
__main__()
  File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 420, 
in __main__
add_file( dataset, registry, json_file, output_path )
  File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 347, 
in add_file
if link_data_only == 'copy_files' and 
datatype.dataset_content_needs_grooming( output_path ):
  File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 
218, in dataset_content_needs_grooming
version = self._get_samtools_version()
  File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 
179, in _get_samtools_version
raise Exception(message)
Exception: Attempting to use functionality requiring samtools, but it cannot be 
located on Galaxy's PATH.

I've checked my installed tools, and all the same Samtools packages are 
successfully installed on the development environment as in production. I don't 
see any missing dependencies or anything like that. At this point I'm stumped. 
If anyone can offer some guidance on how to resolve this, I'd be most 
appreciative.

Best regards,

--
Scott B. Szakonyi
Research Programmer

Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu

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Re: [galaxy-dev] correctly installing to toolshed

[Karen Reddy]

Thanks!

Sent from Nine

From: Gildas Le Corguillé 
Sent: Feb 25, 2016 3:17 PM
To: Karen Reddy
Cc: Xianrong; Björn Grüning; Xianrong Wong; galaxy-...@lists.bx.psu.edu
Subject: Re: [galaxy-dev] correctly installing to toolshed

Hi all,

You will found in attachment the modification, I proposed in my first email.

As I said when your script is near your xml, you just need to use the 
interpreter attribute in 


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[galaxy-dev] Issue with Using Bar

[Harrison Thompson]

Hello,

I am using Galaxy for a school project, but I’m running into an issue with my 
“Using Bar” in the top right corner. I started off running programs at roughly 
30% using. I then downloaded a number of sequences to analyze and went above 
100% on my Using Bar. I then purged the entirety of my history and still am at 
80+% of my Using Bar. Is there something I’m not deleting that I need to? I 
really need it to go down to run my class project, but I’ve tried deleting 
everything, and it’s not working.

Thanks,
Harrison
hmt0003
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Re: [galaxy-dev] Difficulty uploading BAM files

[Christian Brenninkmeijer]

I too had trouble with BAM files as

https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py 
Line 201
class Bam( Binary ):
...
def _get_samtools_version( self ):
...
samtools_exec = which('samtools')

Assumes samtools is installed on the server and was not fining one.

I had to install samtools outside of galaxy to get past that.

Christian
University of Manchester

From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Scott Szakonyi [scott.b.szakony...@nd.edu]
Sent: Friday, February 26, 2016 5:49 PM
To: Galaxy Dev Mailing List
Subject: [galaxy-dev] Difficulty uploading BAM files

Hi,

I'm having trouble uploading BAM files in our development environment. Other 
files types are uploading without issue. I'm testing with a small BAM file I 
downloaded, and I'm able to successfully upload it on our production server and 
usegalaxy.org. When I try to upload in the development 
environment, I get the following error:

Traceback (most recent call last):
  File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 431, 
in 
__main__()
  File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 420, 
in __main__
add_file( dataset, registry, json_file, output_path )
  File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 347, 
in add_file
if link_data_only == 'copy_files' and 
datatype.dataset_content_needs_grooming( output_path ):
  File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 
218, in dataset_content_needs_grooming
version = self._get_samtools_version()
  File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 
179, in _get_samtools_version
raise Exception(message)
Exception: Attempting to use functionality requiring samtools, but it cannot be 
located on Galaxy's PATH.

I've checked my installed tools, and all the same Samtools packages are 
successfully installed on the development environment as in production. I don't 
see any missing dependencies or anything like that. At this point I'm stumped. 
If anyone can offer some guidance on how to resolve this, I'd be most 
appreciative.

Best regards,

--
Scott B. Szakonyi
Research Programmer

Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu
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Re: [galaxy-dev] Difficulty uploading BAM files

[Marius van den Beek]

Hello Scott,

you do need a samtools binary on GALAXY's PATH.
This is not samtools installed from the toolshed.

Best,
Marius

On 26 February 2016 at 18:49, Scott Szakonyi 
wrote:

> Hi,
>
> I'm having trouble uploading BAM files in our development environment.
> Other files types are uploading without issue. I'm testing with a small BAM
> file I downloaded, and I'm able to successfully upload it on our production
> server and usegalaxy.org. When I try to upload in the development
> environment, I get the following error:
>
> Traceback (most recent call last):
>   File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line
> 431, in 
> __main__()
>   File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line
> 420, in __main__
> add_file( dataset, registry, json_file, output_path )
>   File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line
> 347, in add_file
> if link_data_only == 'copy_files' and
> datatype.dataset_content_needs_grooming( output_path ):
>   File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py",
> line 218, in dataset_content_needs_grooming
> version = self._get_samtools_version()
>   File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py",
> line 179, in _get_samtools_version
> raise Exception(message)
> Exception: Attempting to use functionality requiring samtools, but it
> cannot be located on Galaxy's PATH.
>
> I've checked my installed tools, and all the same Samtools packages are
> successfully installed on the development environment as in production. I
> don't see any missing dependencies or anything like that. At this point I'm
> stumped. If anyone can offer some guidance on how to resolve this, I'd be
> most appreciative.
>
> Best regards,
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
>
> ___
> 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] samtools view tools

[Christian Brenninkmeijer]

Hi All,

Has anyone written galaxy tools for the samtools view functions such as

samtools view -f 0x0002 -F 0x0100 -uo

and/or

samtools view -uSo

Thanks
Christian
University of Manchester
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Re: [galaxy-dev] Seeking Job Metrics Clarity

[Ziphozakhe Mashologu]

Hi Nate

Thanks for the response.

It was indeed part of the problem. I needed collectl installed on the
individual cluster instances.(job runners)

Seems to be working properly now. I plan to work on using the metrics to
dynamical & intelligently choose job destination of mapping jobs for
example.

Thanks
Z
On 26 Feb 2016 15:21, "Nate Coraor"  wrote:

> On Wed, Feb 24, 2016 at 5:37 AM, Ziphozakhe Mashologu 
> wrote:
>
>> Hi All
>>
>> I have enabled job metrics on a local galaxy install, with latest code
>> from dev branch. I have " " uncommented in job_metrics_conf.xml
>> file:
>>
>> Following are the errors in the logs:
>>
>> galaxy.jobs.metrics ERROR 2016-02-24 12:28:08,741 Failed to collect job
>> properties for plugin
>> > 0x7ff0b6af3a50>
>> Traceback (most recent call last):
>>   File "dev/galaxy/lib/galaxy/jobs/metrics/__init__.py", line 101, in
>> collect_properties
>> properties = plugin.job_properties( job_id, job_directory )
>>   File "dev/galaxy/lib/galaxy/jobs/metrics/instrumenters/collectl.py",
>> line 105, in job_properties
>> raise Exception( message )
>> Exception: Failed to find collectl log in directory
>>
>> It seems like collectl is looking for the following files:
>>
>> ['__instrument_collectl_pid', '__instrument_env_vars', 'galaxy.json',
>> 'metadata_kwds_HistoryDatasetAssociation_2_1rh1WC',
>> 'set_metadata_N05Q24.py', '__instrument_core_galaxy_slots',
>> 'metadata_results_HistoryDatasetAssociation_2_33gTDj',
>> '__instrument_core_epoch_start', 'galaxy_2.sh',
>> 'metadata_out_HistoryDatasetAssociation_2_G5bZYP',
>> '__instrument_core_epoch_end', '__instrument_meminfo_meminfo',
>> '__instrument_uname_uname',
>> 'metadata_override_HistoryDatasetAssociation_2_krldDM',
>> 'set_metadata_lpIXS5.py', 'metadata_in_HistoryDatasetAssociation_2_iiYW0t',
>> '__instrument_cpuinfo_cpuinfo', 'tool_script.sh', 'galaxy_2.ec']
>>
>> Which are suppose to exist under
>> galaxy/database/job_working_directory/000 job directory.
>>
>> Has anybody faced anything similar issue or is it a configuration issue,
>> or perhaps a known issue with job_metrics (collectl)?
>>
>> BTW: I installed collectl packages on the host.
>>
>
> Hi Zipho,
>
> If this Galaxy instance runs jobs on a cluster, you would also need
> collectl to be installed on the cluster.
>
> --nate
>
>
>
>>
>> Regards
>> Zipho
>>
>>
>> ___
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
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>>   http://galaxyproject.org/search/mailinglists/
>>
>
>
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Re: [galaxy-dev] Seeking Job Metrics Clarity

[Nate Coraor]

On Wed, Feb 24, 2016 at 5:37 AM, Ziphozakhe Mashologu 
wrote:

> Hi All
>
> I have enabled job metrics on a local galaxy install, with latest code
> from dev branch. I have " " uncommented in job_metrics_conf.xml
> file:
>
> Following are the errors in the logs:
>
> galaxy.jobs.metrics ERROR 2016-02-24 12:28:08,741 Failed to collect job
> properties for plugin
>  0x7ff0b6af3a50>
> Traceback (most recent call last):
>   File "dev/galaxy/lib/galaxy/jobs/metrics/__init__.py", line 101, in
> collect_properties
> properties = plugin.job_properties( job_id, job_directory )
>   File "dev/galaxy/lib/galaxy/jobs/metrics/instrumenters/collectl.py",
> line 105, in job_properties
> raise Exception( message )
> Exception: Failed to find collectl log in directory
>
> It seems like collectl is looking for the following files:
>
> ['__instrument_collectl_pid', '__instrument_env_vars', 'galaxy.json',
> 'metadata_kwds_HistoryDatasetAssociation_2_1rh1WC',
> 'set_metadata_N05Q24.py', '__instrument_core_galaxy_slots',
> 'metadata_results_HistoryDatasetAssociation_2_33gTDj',
> '__instrument_core_epoch_start', 'galaxy_2.sh',
> 'metadata_out_HistoryDatasetAssociation_2_G5bZYP',
> '__instrument_core_epoch_end', '__instrument_meminfo_meminfo',
> '__instrument_uname_uname',
> 'metadata_override_HistoryDatasetAssociation_2_krldDM',
> 'set_metadata_lpIXS5.py', 'metadata_in_HistoryDatasetAssociation_2_iiYW0t',
> '__instrument_cpuinfo_cpuinfo', 'tool_script.sh', 'galaxy_2.ec']
>
> Which are suppose to exist under galaxy/database/job_working_directory/000
> job directory.
>
> Has anybody faced anything similar issue or is it a configuration issue,
> or perhaps a known issue with job_metrics (collectl)?
>
> BTW: I installed collectl packages on the host.
>

Hi Zipho,

If this Galaxy instance runs jobs on a cluster, you would also need
collectl to be installed on the cluster.

--nate



>
> Regards
> Zipho
>
>
> ___
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[galaxy-dev] Downgrade tool upload tool

[Makis Ladoukakis]

Hello everyone,

I was wondering whether it's possible to downgrade the upload tool to the 
previous version(1.1.4).

I copied the upload.py and upload.xml scripts from a previous galaxy version to 
the tools/data_source/ directory and reloaded the tool as admin but it hasn't 
changed even when I restarted the server. 

Do I have to change something else in addition?

Thank you,
Makis
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Re: [galaxy-dev] packaging R scripts

[Gildas Le Corguillé]

Hi,

For me, three solutions :
 - You can find existing packages which will install your library 
(https://testtoolshed.g2.bx.psu.edu/view/jeltje/package_dnacopy_1_40_0/118417199f06
 
).
 So you will just need to link a requirement 
(https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Crequirements.3E_tag_set
 
)
 and a tool_dependencies.xml file
 - If not, you can write your own package. But thanks to Ross Lazarus, to deal 
with dependencies of dependencies of dependencies, there is a tool for that 
https://testtoolshed.g2.bx.psu.edu/view/fubar/biocdepgen_r_3_1_2/faafc60f3d6a 

 - If you lack of time, you install R and needed libraries on your serveur.

Unfortunately, I can’t explain you why you couldn’t install your library 
through your script because R use to allow installing in the user home.


Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr
--



> Le 26 févr. 2016 à 09:03, Xianrong Wong  a écrit :
> 
> Hi,
> I am trying to package an R script (that requires certain R packages) 
> into a galaxy tool.  Any advice would be deeply appreciated!  
> 
> I have tested it on planemo and it works.  When I tried the version I 
> uploaded onto the toolshed, I got an error saying that the R packages do not 
> exist.  I next added the following lines to the R script:
> 
> source("https://bioconductor.org/biocLite.R 
> ")
> 
> biocLite()
> 
> biocLite(c("DNAcopy", "preprocessCore"))
> 
> and I got the following error when running the installed tool on galaxy:
> 
> 
> 
> Installing package(s) ‘DNAcopy’, ‘preprocessCore’
> Warning in install.packages(pkgs = doing, lib = lib, ...) :
>   'lib = "/usr/local/lib/R/site-library"' is not writable
> Error in install.packages(pkgs = doing, lib = lib, ...) : 
>   unable to install packages
> Calls: biocLite ... .biocLiteInstall -> .reposInstall -> install.packages
> Execution halted
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[galaxy-dev] packaging R scripts

[Xianrong Wong]

Hi,
I am trying to package an R script (that requires certain R packages)
into a galaxy tool.  Any advice would be deeply appreciated!

I have tested it on planemo and it works.  When I tried the version I
uploaded onto the toolshed, I got an error saying that the R packages do
not exist.  I next added the following lines to the R script:

source("https://bioconductor.org/biocLite.R;)

biocLite()

biocLite(c("DNAcopy", "preprocessCore"))

and I got the following error when running the installed tool on galaxy:


Installing package(s) ‘DNAcopy’, ‘preprocessCore’
Warning in install.packages(pkgs = doing, lib = lib, ...) :
  'lib = "/usr/local/lib/R/site-library"' is not writable
Error in install.packages(pkgs = doing, lib = lib, ...) :
  unable to install packages
Calls: biocLite ... .biocLiteInstall -> .reposInstall -> install.packages
Execution halted
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