[galaxy-dev] Bioconductor packages in Galaxy

[Deepak Tanwar]

Hi,

I am using galaxy via Docker.
I cannot find saw package on galaxy toolshed. It is available on bioconda: 
https://bioconda.github.io/recipes/bioconductor-csaw/README.html

How can I use it Galaxy?

Thank you,
Deepak


On Nov 22, 2017, at 05:03, Gildas Le Corguillé 
mailto:lecorgui...@sb-roscoff.fr>> wrote:

Salut Nils,

I think that you should take a look at the Galaxy Interactive Environment (GIE):
 - https://docs.galaxyproject.org/en/master/admin/interactive_environments.html
 - 
https://galaxyproject.github.io/training-material/topics/dev/tutorials/interactive-environments/slides.html

Cheers

Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--



Le 15 nov. 2017 à 09:26, Nils Paulhe 
mailto:nils.pau...@gmail.com>> a écrit :

Dear list,

I'm working on data visualization / display in galaxy.
I'm wondering if it's possible to save a resource edited from the viewer plugin 
or an external display in the current history.
In my opinion the easier / proper way is to use an external display to show / 
edit the resources and upload the edited files in the current history using 
galaxy API.

Does anyone have tried something similar?
Cheers

Nils
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Re: [galaxy-dev] Job error

[Deepak Tanwar]

Sorry, forgot to attach the error file!




On Oct 20, 2017, at 12:21 PM, Deepak Tanwar 
mailto:dktan...@hotmail.com>> wrote:

Hi all,

I am facing some problem in building a galaxy tool from Rscript (using planemo).
The error file is attached.

Main error is: dyld: Library not loaded: @rpath/libintl.8.dylib
I have tried suggestions from: 
https://github.com/tectonic-typesetting/tectonic/issues/40

Thank you,
Deepak


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[galaxy-dev] Job error

[Deepak Tanwar]

Hi all,

I am facing some problem in building a galaxy tool from Rscript (using planemo).
The error file is attached.

Main error is: dyld: Library not loaded: @rpath/libintl.8.dylib
I have tried suggestions from: 
https://github.com/tectonic-typesetting/tectonic/issues/40

Thank you,
Deepak


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Re: [galaxy-dev] MACS2 Error

[Deepak Tanwar]

I am using Galaxy via Docker.

On Oct 18, 2017, at 11:51 AM, Devon Ryan 
mailto:dprya...@gmail.com>> wrote:


Assuming you don't have galaxy set to clean up job working directories upon 
failure, have a look at the tool_script.sh in that directory and see if you can 
discern the issue. Also check the conda activation log file (under working/ I 
think) in that directory to see if it has anything useful.

Devon

On 10/18/2017 05:46 PM, Deepak Tanwar wrote:
Hello,

I am still facing problem. I have tried to reinstall MACS2 but nothing helped.

Thank you!
Deepak


On Oct 16, 2017, at 4:00 PM, Deepak Tanwar 
mailto:dktan...@hotmail.com>> wrote:

Hi all,

There is some problem with MACS2:

export/galaxy-central/database/job_working_directory/000/380/tool_script.sh: 
line 25: macs2: command not found Fatal error: Exit code 127 ()
Tool installed: 
/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2<http://toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2>

Dependency Resolver Details
Dependency  Version ResolverExact version   Current Installation 
Status

macs2   2.1.1.20160309  Conda   True
[http://192.168.99.100:32811/static/june_2007_style/blue/ok_small.png]
gawk4.1.3   Conda   True
[http://192.168.99.100:32811/static/june_2007_style/blue/ok_small.png]



Thank you,
Deepak




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--
Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: dprya...@gmail.com<mailto:dprya...@gmail.com>

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Re: [galaxy-dev] MACS2 Error

[Deepak Tanwar]

Hello,

I am still facing problem. I have tried to reinstall MACS2 but nothing helped.

Thank you!
Deepak


On Oct 16, 2017, at 4:00 PM, Deepak Tanwar 
mailto:dktan...@hotmail.com>> wrote:

Hi all,

There is some problem with MACS2:

export/galaxy-central/database/job_working_directory/000/380/tool_script.sh: 
line 25: macs2: command not found Fatal error: Exit code 127 ()

Tool installed: 
/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2<http://toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2>

Dependency Resolver Details
Dependency  Version ResolverExact version   Current Installation 
Status
macs2   2.1.1.20160309  Conda   True
[http://192.168.99.100:32811/static/june_2007_style/blue/ok_small.png]
gawk4.1.3   Conda   True
[http://192.168.99.100:32811/static/june_2007_style/blue/ok_small.png]



Thank you,
Deepak

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[galaxy-dev] MACS2 Error

[Deepak Tanwar]

Hi all,

There is some problem with MACS2:

export/galaxy-central/database/job_working_directory/000/380/tool_script.sh: 
line 25: macs2: command not found Fatal error: Exit code 127 ()

Tool installed: 
/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2

Dependency Resolver Details
Dependency  Version ResolverExact version   Current Installation 
Status
macs2   2.1.1.20160309  Conda   True
[http://192.168.99.100:32811/static/june_2007_style/blue/ok_small.png]
gawk4.1.3   Conda   True
[http://192.168.99.100:32811/static/june_2007_style/blue/ok_small.png]



Thank you,
Deepak
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[galaxy-dev] plane error for Rscript

[Deepak Tanwar]

Hello everyone,

I have a question about https://github.com/nturaga/bioc-galaxy-integration  I 
am trying to convert a RScript into a Galaxy tool.

planemo bioc_tool_init --rscript ./countsAroundTSS.R --input ENCFF027UTM.bam 
--input mm10 --input 500 --input 500 --input transcripts_mm10_UCSC.sqlite 
--output ENCFF027UTM.txt --test_case
Can only use the --test_case option if also specifying --example_command


planemo bioc_tool_init --rscript ./countsAroundTSS.R --example_command "Rscript 
countsAroundTSS.R--input ENCFF027UTM.bam --input mm10 --input 500 --input 500 
--input transcripts_mm10_UCSC.sqlite --output ENCFF027UTM.txt”
Error: no such option: --example_command


I am able to build a tool is I just run planemo bioc_tool_init --rscript 
./countsAroundTSS.R --input ENCFF027UTM.bam --input mm10 --input 500 --input 
500 --input transcripts_mm10_UCSC.sqlite --output ENCFF027UTM.txt



https://github.com/galaxyproject/planemo/issues/718


Thank you,
Deepak

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Re: [galaxy-dev] Samtools problem in Docker

[Deepak Tanwar]

Hi Björn,

I tried again from scratch.

1. I have installed galaxy-stable image via Kitematic.
2. I install samtools: package_samtools_1_2 (2015-07-17) iuc
3. I have uploaded the bam file. Error:


Traceback (most recent call last):
  File "/galaxy-central/tools/data_source/upload.py", line 425, in 
__main__()
  File "/galaxy-central/tools/data_source/upload.py", line 413, in __main__
add_file( dataset, registry, json_file, output_path )
  File "/galaxy-central/tools/data_source/upload.py", line 340, in add_file
if link_data_only == 'copy_files' and 
datatype.dataset_content_needs_grooming( output_path ):
  File "/galaxy-central/lib/galaxy/datatypes/binary.py", line 295, in 
dataset_content_needs_grooming
version = self._get_samtools_version()
  File "/galaxy-central/lib/galaxy/datatypes/binary.py", line 244, in 
_get_samtools_version
raise Exception(message)
Exception: Attempting to use functionality requiring samtools, but it cannot be 
located on Galaxy's PATH.

4. I restarted the galaxy and the uploaded the bam file. Error:


Traceback (most recent call last):
  File "/galaxy-central/tools/data_source/upload.py", line 425, in 
__main__()
  File "/galaxy-central/tools/data_source/upload.py", line 413, in __main__
add_file( dataset, registry, json_file, output_path )
  File "/galaxy-central/tools/data_source/upload.py", line 340, in add_file
if link_data_only == 'copy_files' and 
datatype.dataset_content_needs_grooming( output_path ):
  File "/galaxy-central/lib/galaxy/datatypes/binary.py", line 295, in 
dataset_content_needs_grooming
version = self._get_samtools_version()
  File "/galaxy-central/lib/galaxy/datatypes/binary.py", line 244, in 
_get_samtools_version
raise Exception(message)
Exception: Attempting to use functionality requiring samtools, but it cannot be 
located on Galaxy's PATH.

5. Now, I installed  suite_samtools_1_2 (2015-04-27) devteam and updated the 
packages. File uploaded successfully!





On Aug 14, 2017, at 16:58, Björn Grüning 
mailto:bjoern.gruen...@gmail.com>> wrote:

Hi Deepak,

as Peter mentioned the Galaxy Docker container can be used as it is.
Can you provide the original error message from the TS?

Cheers,
Bjoern

On 14.08.2017 18:17, Deepak Tanwar wrote:
I am using https://hub.docker.com/r/bgruening/galaxy-stable

I aded path to the samtools because I was getting error after installing
samtools from toolshed.

Thank you,
Deepak

On Aug 14, 2017, at 12:10, Peter Cock 
mailto:p.j.a.c...@googlemail.com>
<mailto:p.j.a.c...@googlemail.com>> wrote:

Galaxy itself uses samtools for many operations, which is different
from when samtools is called as a dependency of a tool run by the
Galaxy user.

However, the Docker image ought to take care of that - can you
give more details of which Docker image you are using (URL,
version, etc)?

Thanks,

Peter


On Mon, Aug 14, 2017 at 5:08 PM, Deepak Tanwar 
mailto:dktan...@hotmail.com>
<mailto:dktan...@hotmail.com>> wrote:
Hello everyone,

I am facing problem in uploading bam files on Galaxy. I am using Docker
image of Galaxy.

I have installed samtools version 0.1.19 and added it to the path
/tool_deps/samtools/0.1.19/iuc/package_samtools_0_1_19/c9bd782f5342/bin/samtools

Error: Exception: Attempting to use functionality requiring samtools,
but it
cannot be located on Galaxy's PATH.

Thank you,
Deepak

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Re: [galaxy-dev] Samtools problem in Docker

[Deepak Tanwar]

I am using https://hub.docker.com/r/bgruening/galaxy-stable

I aded path to the samtools because I was getting error after installing 
samtools from toolshed.

Thank you,
Deepak

On Aug 14, 2017, at 12:10, Peter Cock 
mailto:p.j.a.c...@googlemail.com>> wrote:

Galaxy itself uses samtools for many operations, which is different
from when samtools is called as a dependency of a tool run by the
Galaxy user.

However, the Docker image ought to take care of that - can you
give more details of which Docker image you are using (URL,
version, etc)?

Thanks,

Peter


On Mon, Aug 14, 2017 at 5:08 PM, Deepak Tanwar 
mailto:dktan...@hotmail.com>> wrote:
Hello everyone,

I am facing problem in uploading bam files on Galaxy. I am using Docker
image of Galaxy.

I have installed samtools version 0.1.19 and added it to the path
/tool_deps/samtools/0.1.19/iuc/package_samtools_0_1_19/c9bd782f5342/bin/samtools

Error: Exception: Attempting to use functionality requiring samtools, but it
cannot be located on Galaxy's PATH.

Thank you,
Deepak

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[galaxy-dev] Samtools problem in Docker

[Deepak Tanwar]

Hello everyone,

I am facing problem in uploading bam files on Galaxy. I am using Docker image 
of Galaxy.

I have installed samtools version 0.1.19 and added it to the path 
/tool_deps/samtools/0.1.19/iuc/package_samtools_0_1_19/c9bd782f5342/bin/samtools

Error: Exception: Attempting to use functionality requiring samtools, but it 
cannot be located on Galaxy's PATH.

Thank you,
Deepak
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Re: [galaxy-dev] Bowtie2 index building

[Deepak Tanwar]

Hi Björn,

That’s right! It was quiet strange. I need to extend the memory and cores usage 
via command line.

Thank you so much!

Deepak


> On Aug 11, 2017, at 10:00, Björn Grüning  wrote:
> 
> Hi,
> 
> it seems that your Docker Box only gets 1GB :(
> 
> please re-check the configs.
> Sorry to be not more helpful!
> Bjoern
> 
> On 11.08.2017 15:55, Deepak Tanwar wrote:
>> Also, I am running this container on a Mac Pro using Kitematic and I
>> have docker preference set to use 12 cores and 64 GB RAM.
>> 
>> Thanks,
>> Deepak
>> 
>> 
>>> On Aug 11, 2017, at 9:54 AM, Deepak Tanwar >> <mailto:dktan...@hotmail.com>> wrote:
>>> 
>>> Hi Björn,
>>> 
>>> If I do docker stats:
>>> CONTAINER   CPU %   MEM USAGE / LIMIT MEM %  
>>>NET I/O BLOCK I/O   PIDS
>>> dd4da10c0a546.16%   690.9MiB / 995.8MiB   69.38%  
>>>   158kB / 785kB   11.4GB / 81MB   106
>>> 
>>> And, after ssh into docker machine:
>>> 
>>> FilesystemSize  Used Available Use% Mounted on
>>> tmpfs   896.2M186.6M709.6M  21% /
>>> tmpfs   497.9M476.0K497.4M   0% /dev/shm
>>> /dev/sda1   282.7G 14.9G253.2G   6% /mnt/sda1
>>> cgroup  497.9M 0497.9M   0% /sys/fs/cgroup
>>> Users   931.0G683.8G247.2G  73% /Users
>>> /dev/sda1   282.7G 14.9G253.2G   6%
>>> /mnt/sda1/var/lib/docker/aufs
>>> 
>>> Best regards,
>>> Deepak
>>> 
>>> 
>>>> On Aug 11, 2017, at 9:39 AM, Björn Grüning >>> <mailto:bjoern.gruen...@gmail.com>> wrote:
>>>> 
>>>> Hi Deepak,
>>>> 
>>>> how are you running this Container?
>>>> Can you check how many memory you have inside the container?
>>>> 
>>>> Cheers,
>>>> Bjoern
>>>> 
>>>> On 11.08.2017 15:35, Deepak Tanwar wrote:
>>>>> Hello,
>>>>> 
>>>>> I am trying to build Bowtie2 index for hg19.
>>>>> I a using Docker image of Galaxy.
>>>>> 
>>>>> Computer I am using have 12 cores and 64 GB of RAM.
>>>>> 
>>>>> Error I am getting is:
>>>>> 
>>>>> Fatal error: Exit code 1 ()
>>>>> Building a SMALL index
>>>>> Could not allocate space for a joined string of 2897310462 elements.
>>>>> Switching to a packed string representation.
>>>>> Building a SMALL index
>>>>> Could not find approrpiate bmax/dcv settings for building this index.
>>>>> Already tried a packed string representation.
>>>>> Please try indexing this reference on a computer with more memory.
>>>>> Error: Encountered internal Bowtie 2 exception (#1)
>>>>> Command: bowtie2-build --wrapper basic-0
>>>>> /export/galaxy-central/database/job_working_directory/000/113/dataset_80_files/hg19
>>>>> fa.fa hg19 fa
>>>>> Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
>>>>> Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
>>>>> Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
>>>>> Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
>>>>> Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
>>>>> Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
>>>>> Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
>>>>> Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
>>>>> Error building index.
>>>>> 
>>>>> Please help!
>>>>> 
>>>>> Thank you,
>>>>> Deepak
>>>>> 
>>>>> 
>>>>> 
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Re: [galaxy-dev] Bowtie2 index building

[Deepak Tanwar]

Also, I am running this container on a Mac Pro using Kitematic and I have 
docker preference set to use 12 cores and 64 GB RAM.

Thanks,
Deepak


On Aug 11, 2017, at 9:54 AM, Deepak Tanwar 
mailto:dktan...@hotmail.com>> wrote:

Hi Björn,

If I do docker stats:
CONTAINER   CPU %   MEM USAGE / LIMIT MEM % 
  NET I/O BLOCK I/O   PIDS
dd4da10c0a546.16%   690.9MiB / 995.8MiB   69.38%
  158kB / 785kB   11.4GB / 81MB   106

And, after ssh into docker machine:

FilesystemSize  Used Available Use% Mounted on
tmpfs   896.2M186.6M709.6M  21% /
tmpfs   497.9M476.0K497.4M   0% /dev/shm
/dev/sda1   282.7G 14.9G253.2G   6% /mnt/sda1
cgroup  497.9M 0497.9M   0% /sys/fs/cgroup
Users   931.0G683.8G247.2G  73% /Users
/dev/sda1   282.7G 14.9G253.2G   6% 
/mnt/sda1/var/lib/docker/aufs

Best regards,
Deepak


On Aug 11, 2017, at 9:39 AM, Björn Grüning 
mailto:bjoern.gruen...@gmail.com>> wrote:

Hi Deepak,

how are you running this Container?
Can you check how many memory you have inside the container?

Cheers,
Bjoern

On 11.08.2017 15:35, Deepak Tanwar wrote:
Hello,

I am trying to build Bowtie2 index for hg19.
I a using Docker image of Galaxy.

Computer I am using have 12 cores and 64 GB of RAM.

Error I am getting is:

Fatal error: Exit code 1 ()
Building a SMALL index
Could not allocate space for a joined string of 2897310462 elements.
Switching to a packed string representation.
Building a SMALL index
Could not find approrpiate bmax/dcv settings for building this index.
Already tried a packed string representation.
Please try indexing this reference on a computer with more memory.
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-build --wrapper basic-0
/export/galaxy-central/database/job_working_directory/000/113/dataset_80_files/hg19
fa.fa hg19 fa
Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
Error building index.

Please help!

Thank you,
Deepak



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Re: [galaxy-dev] Bowtie2 index building

[Deepak Tanwar]

Hi Björn,

If I do docker stats:
CONTAINER   CPU %   MEM USAGE / LIMIT MEM % 
  NET I/O BLOCK I/O   PIDS
dd4da10c0a546.16%   690.9MiB / 995.8MiB   69.38%
  158kB / 785kB   11.4GB / 81MB   106

And, after ssh into docker machine:

FilesystemSize  Used Available Use% Mounted on
tmpfs   896.2M186.6M709.6M  21% /
tmpfs   497.9M476.0K497.4M   0% /dev/shm
/dev/sda1   282.7G 14.9G253.2G   6% /mnt/sda1
cgroup  497.9M 0497.9M   0% /sys/fs/cgroup
Users   931.0G683.8G247.2G  73% /Users
/dev/sda1   282.7G 14.9G253.2G   6% 
/mnt/sda1/var/lib/docker/aufs

Best regards,
Deepak


On Aug 11, 2017, at 9:39 AM, Björn Grüning 
mailto:bjoern.gruen...@gmail.com>> wrote:

Hi Deepak,

how are you running this Container?
Can you check how many memory you have inside the container?

Cheers,
Bjoern

On 11.08.2017 15:35, Deepak Tanwar wrote:
Hello,

I am trying to build Bowtie2 index for hg19.
I a using Docker image of Galaxy.

Computer I am using have 12 cores and 64 GB of RAM.

Error I am getting is:

Fatal error: Exit code 1 ()
Building a SMALL index
Could not allocate space for a joined string of 2897310462 elements.
Switching to a packed string representation.
Building a SMALL index
Could not find approrpiate bmax/dcv settings for building this index.
Already tried a packed string representation.
Please try indexing this reference on a computer with more memory.
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-build --wrapper basic-0
/export/galaxy-central/database/job_working_directory/000/113/dataset_80_files/hg19
fa.fa hg19 fa
Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
Error building index.

Please help!

Thank you,
Deepak



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[galaxy-dev] Bowtie2 index building

[Deepak Tanwar]

Hello,

I am trying to build Bowtie2 index for hg19.
I a using Docker image of Galaxy.

Computer I am using have 12 cores and 64 GB of RAM.

Error I am getting is:

Fatal error: Exit code 1 ()
Building a SMALL index
Could not allocate space for a joined string of 2897310462 elements.
Switching to a packed string representation.
Building a SMALL index
Could not find approrpiate bmax/dcv settings for building this index.
Already tried a packed string representation.
Please try indexing this reference on a computer with more memory.
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-build --wrapper basic-0 
/export/galaxy-central/database/job_working_directory/000/113/dataset_80_files/hg19
 fa.fa hg19 fa
Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
Error building index.

Please help!

Thank you,
Deepak

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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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