GATK2

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GATK2

Briand, Sheldon

Hi,

 

I’ve installed the latest version (using GATK2.8-1) of the GATK2 wrapper here.  I’ve run into the following error:

##### ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-V7IrBw) does not exist.

 

I see via much googling that this error is due to a user input problem.  I’ve tried pointing the gatk2_picard_index.loc file in tool-data to the proper data files:

hg19 hg19    hg19    /software/packages/galaxy/data/picard/hg19.fa

 

where the following files exist:

hg19.dict

hg19.fa

hg19.fa.fai

 

I’m using a torque setup.  A bam file is being used as input.  After much trial and error I’ve been unable to figure out what I’m missing. 

 

None of the solutions on google apply to my situation.

 

Has anyone else run into this configuration problem and solved it?

 

Thanks,

-Sheldon

 

Sheldon Briand

NRC Research Computing Support Analyst

Research Computing Support / Soutien Informartique a la Recherche

Operations, Science Portfolio / Operations, Portefeuil des sciences

SSC-NRC / SPC-CNRC

Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford

Halifax, NS  B3H 3Z1

902 426-1677

[hidden email]

 


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Re: GATK2

Björn Grüning-3
Hi,

do you have access to the generated commandline from Galaxy and can
paste it her?

>
> I’ve installed the latest version (using GATK2.8-1) of the GATK2
> wrapper here.  I’ve run into the following error:
>
> ##### ERROR MESSAGE: The fasta file you specified
> (/tmp/tmp-gatk-V7IrBw) does not exist.
>
>  
>
> I see via much googling that this error is due to a user input
> problem.  I’ve tried pointing the gatk2_picard_index.loc file in
> tool-data to the proper data files:
>
> hg19 hg19    hg19    /software/packages/galaxy/data/picard/hg19.fa

That look ok, as far as every token is separated by a tabular.

>
> where the following files exist:
>
> hg19.dict
>
> hg19.fa
>
> hg19.fa.fai

Can you put the 2bit file into the same folder?

Cheers,
Bjoern


>
> I’m using a torque setup.  A bam file is being used as input.  After
> much trial and error I’ve been unable to figure out what I’m
> missing.  
>
>  
>
> None of the solutions on google apply to my situation.
>
>  
>
> Has anyone else run into this configuration problem and solved it?
>
>  
>
> Thanks,
>
> -Sheldon
>
>  
>
> Sheldon Briand
>
> NRC Research Computing Support Analyst
>
> Research Computing Support / Soutien Informartique a la Recherche
>
> Operations, Science Portfolio / Operations, Portefeuil des sciences
>
> SSC-NRC / SPC-CNRC
>
> Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
>
> Halifax, NS  B3H 3Z1
>
> 902 426-1677
>
> [hidden email]
>
>  
>
>
> ___________________________________________________________
> 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:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/


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Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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Re: GATK2

Briand, Sheldon
Hi Bjoern,

The loc file is tabular.  I put the 2bit file in the directory and had no success.  Here is the rather lengthy commandline:

#!/bin/sh

export GALAXY_SLOTS_CONFIGURED="1"
if [ -n "$SLURM_JOB_NUM_NODES" ]; then
    GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"
elif [ -n "$NSLOTS" ]; then
    GALAXY_SLOTS="$NSLOTS"
elif [ -f "$PBS_NODEFILE" ]; then
    GALAXY_SLOTS=`wc -l < $PBS_NODEFILE`
else
    GALAXY_SLOTS="1"
    unset GALAXY_SLOTS_CONFIGURED
fi

export GALAXY_SLOTS
GALAXY_LIB="/software/packages/galaxy/galaxy-dist/lib"
if [ "$GALAXY_LIB" != "None" ]; then
    if [ -n "$PYTHONPATH" ]; then
        PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
    else
        PYTHONPATH="$GALAXY_LIB"
    fi
    export PYTHONPATH
fi

[ -f "/home/galaxy/.bashrc" ] && . /home/galaxy/.bashrc
cd /software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101
PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc/gatk2/8bcc13094767; export PACKA
GE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc/gatk2/8bcc13094767/env.sh; PACKAGE
_BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_settings/GATK2_PATH/iuc/gatk2/8bcc13094767; exp
ort PACKAGE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/environment_settings/GATK2_PATH/iuc/gatk2/8bc
c13094767/env.sh; PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_settings/GATK2_SITE_OP
TIONS/iuc/gatk2/8bcc13094767; export PACKAGE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/environment_
settings/GATK2_SITE_OPTIONS/iuc/gatk2/8bcc13094767/env.sh; python /software/packages/galaxy/shed_tools/toolshed.g2.b
x.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py     --stdout "/software/packages/galaxy/galaxy-dist/da
tabase/files/000/dataset_126.dat"     -d "-I" "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_114.
dat" "bam" "gatk_input"         -d "" "/software/packages/galaxy/galaxy-dist/database/files/_metadata_files/000/meta
data_19.dat" "bam_index" "gatk_input"      -p '          java -jar "$GATK2_PATH/GenomeAnalysisTK.jar"        -T "Rea
lignerTargetCreator"     -o "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_125.dat"      $GATK2_S
ITE_OPTIONS      --num_cpu_threads_per_data_thread 1           --num_threads ${GALAXY_SLOTS:-4}             -R ""  
 '; return_code=$?; cd /software/packages/galaxy/galaxy-dist; /software/packages/galaxy/galaxy-dist/set_metadata.sh
./database/files /software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101 . /software/packages/g
alaxy/galaxy-dist/universe_wsgi.ini /software/packages/galaxy/galaxy-dist/database/tmp/tmpfjJAKX /software/packages/
galaxy/galaxy-dist/database/job_working_directory/000/101/galaxy.json /software/packages/galaxy/galaxy-dist/database
/job_working_directory/000/101/metadata_in_HistoryDatasetAssociation_102_DXIvP5,/software/packages/galaxy/galaxy-dis
t/database/job_working_directory/000/101/metadata_kwds_HistoryDatasetAssociation_102_ifJAbu,/software/packages/galax
y/galaxy-dist/database/job_working_directory/000/101/metadata_out_HistoryDatasetAssociation_102_Ie2O0C,/software/pac
kages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_results_HistoryDatasetAssociation_102_xLNtK
a,,/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_override_HistoryDatasetAsso
ciation_102__IZJ7Y /software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_in_HistoryD
atasetAssociation_103_uoVLce,/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_k
wds_HistoryDatasetAssociation_103_1e5Jn2,/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/10
1/metadata_out_HistoryDatasetAssociation_103_NNh80i,/software/packages/galaxy/galaxy-dist/database/job_working_direc
tory/000/101/metadata_results_HistoryDatasetAssociation_103_ZVuezG,,/software/packages/galaxy/galaxy-dist/database/j
ob_working_directory/000/101/metadata_override_HistoryDatasetAssociation_103_LFaURY; sh -c "exit $return_code"
echo $? > /software/packages/galaxy/galaxy-dist/database/pbs/101.ec

Thanks,
-Sheldon

-----Original Message-----
From: Björn Grüning [mailto:[hidden email]]
Sent: Thursday, January 30, 2014 12:26 PM
To: Briand, Sheldon
Cc: [hidden email]
Subject: Re: [galaxy-dev] GATK2

Hi,

do you have access to the generated commandline from Galaxy and can paste it her?

>
> I’ve installed the latest version (using GATK2.8-1) of the GATK2
> wrapper here.  I’ve run into the following error:
>
> ##### ERROR MESSAGE: The fasta file you specified
> (/tmp/tmp-gatk-V7IrBw) does not exist.
>
>  
>
> I see via much googling that this error is due to a user input
> problem.  I’ve tried pointing the gatk2_picard_index.loc file in
> tool-data to the proper data files:
>
> hg19 hg19    hg19    /software/packages/galaxy/data/picard/hg19.fa

That look ok, as far as every token is separated by a tabular.

>
> where the following files exist:
>
> hg19.dict
>
> hg19.fa
>
> hg19.fa.fai

Can you put the 2bit file into the same folder?

Cheers,
Bjoern


>
> I’m using a torque setup.  A bam file is being used as input.  After
> much trial and error I’ve been unable to figure out what I’m missing.
>
>  
>
> None of the solutions on google apply to my situation.
>
>  
>
> Has anyone else run into this configuration problem and solved it?
>
>  
>
> Thanks,
>
> -Sheldon
>
>  
>
> Sheldon Briand
>
> NRC Research Computing Support Analyst
>
> Research Computing Support / Soutien Informartique a la Recherche
>
> Operations, Science Portfolio / Operations, Portefeuil des sciences
>
> SSC-NRC / SPC-CNRC
>
> Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
>
> Halifax, NS  B3H 3Z1
>
> 902 426-1677
>
> [hidden email]
>
>  
>
>
> ___________________________________________________________
> 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:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: GATK2

Björn Grüning-3
Hi Sheldon,

> The loc file is tabular.  I put the 2bit file in the directory and had no success.  Here is the rather lengthy commandline:
>
> #!/bin/sh
>
> export GALAXY_SLOTS_CONFIGURED="1"
> if [ -n "$SLURM_JOB_NUM_NODES" ]; then
>     GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"
> elif [ -n "$NSLOTS" ]; then
>     GALAXY_SLOTS="$NSLOTS"
> elif [ -f "$PBS_NODEFILE" ]; then
>     GALAXY_SLOTS=`wc -l < $PBS_NODEFILE`
> else
>     GALAXY_SLOTS="1"
>     unset GALAXY_SLOTS_CONFIGURED
> fi
>
> export GALAXY_SLOTS
> GALAXY_LIB="/software/packages/galaxy/galaxy-dist/lib"
> if [ "$GALAXY_LIB" != "None" ]; then
>     if [ -n "$PYTHONPATH" ]; then
>         PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
>     else
>         PYTHONPATH="$GALAXY_LIB"
>     fi
>     export PYTHONPATH
> fi
>
> [ -f "/home/galaxy/.bashrc" ] && . /home/galaxy/.bashrc
> cd /software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101
> PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc/gatk2/8bcc13094767; export PACKA
> GE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc/gatk2/8bcc13094767/env.sh; PACKAGE
> _BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_settings/GATK2_PATH/iuc/gatk2/8bcc13094767; exp
> ort PACKAGE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/environment_settings/GATK2_PATH/iuc/gatk2/8bc
> c13094767/env.sh; PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_settings/GATK2_SITE_OP
> TIONS/iuc/gatk2/8bcc13094767; export PACKAGE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/environment_
> settings/GATK2_SITE_OPTIONS/iuc/gatk2/8bcc13094767/env.sh; python /software/packages/galaxy/shed_tools/toolshed.g2.b
> x.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py     --stdout "/software/packages/galaxy/galaxy-dist/da
> tabase/files/000/dataset_126.dat"     -d "-I" "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_114.
> dat" "bam" "gatk_input"         -d "" "/software/packages/galaxy/galaxy-dist/database/files/_metadata_files/000/meta
> data_19.dat" "bam_index" "gatk_input"      -p '          java -jar "$GATK2_PATH/GenomeAnalysisTK.jar"        -T "Rea
> lignerTargetCreator"     -o "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_125.dat"      $GATK2_S
> ITE_OPTIONS      --num_cpu_threads_per_data_thread 1           --num_threads ${GALAXY_SLOTS:-4}            


>  -R ""

-> that is the error. Here needs to be your path to the fasta file. Can
you point to me to Tool Shed Version you are using and are you running
the latest revision? Do you see hg19 / hg18 in the select-box under
"using-reference genome"

Can you attach your gatk2_picard_index.loc?

Thanks,
Bjoern

>  
>  '; return_code=$?; cd /software/packages/galaxy/galaxy-dist; /software/packages/galaxy/galaxy-dist/set_metadata.sh
> ./database/files /software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101 . /software/packages/g
> alaxy/galaxy-dist/universe_wsgi.ini /software/packages/galaxy/galaxy-dist/database/tmp/tmpfjJAKX /software/packages/
> galaxy/galaxy-dist/database/job_working_directory/000/101/galaxy.json /software/packages/galaxy/galaxy-dist/database
> /job_working_directory/000/101/metadata_in_HistoryDatasetAssociation_102_DXIvP5,/software/packages/galaxy/galaxy-dis
> t/database/job_working_directory/000/101/metadata_kwds_HistoryDatasetAssociation_102_ifJAbu,/software/packages/galax
> y/galaxy-dist/database/job_working_directory/000/101/metadata_out_HistoryDatasetAssociation_102_Ie2O0C,/software/pac
> kages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_results_HistoryDatasetAssociation_102_xLNtK
> a,,/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_override_HistoryDatasetAsso
> ciation_102__IZJ7Y /software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_in_HistoryD
> atasetAssociation_103_uoVLce,/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_k
> wds_HistoryDatasetAssociation_103_1e5Jn2,/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/10
> 1/metadata_out_HistoryDatasetAssociation_103_NNh80i,/software/packages/galaxy/galaxy-dist/database/job_working_direc
> tory/000/101/metadata_results_HistoryDatasetAssociation_103_ZVuezG,,/software/packages/galaxy/galaxy-dist/database/j
> ob_working_directory/000/101/metadata_override_HistoryDatasetAssociation_103_LFaURY; sh -c "exit $return_code"
> echo $? > /software/packages/galaxy/galaxy-dist/database/pbs/101.ec
>
> Thanks,
> -Sheldon
>
> -----Original Message-----
> From: Björn Grüning [mailto:[hidden email]]
> Sent: Thursday, January 30, 2014 12:26 PM
> To: Briand, Sheldon
> Cc: [hidden email]
> Subject: Re: [galaxy-dev] GATK2
>
> Hi,
>
> do you have access to the generated commandline from Galaxy and can paste it her?
>
> >
> > I’ve installed the latest version (using GATK2.8-1) of the GATK2
> > wrapper here.  I’ve run into the following error:
> >
> > ##### ERROR MESSAGE: The fasta file you specified
> > (/tmp/tmp-gatk-V7IrBw) does not exist.
> >
> >  
> >
> > I see via much googling that this error is due to a user input
> > problem.  I’ve tried pointing the gatk2_picard_index.loc file in
> > tool-data to the proper data files:
> >
> > hg19 hg19    hg19    /software/packages/galaxy/data/picard/hg19.fa
>
> That look ok, as far as every token is separated by a tabular.
>
> >
> > where the following files exist:
> >
> > hg19.dict
> >
> > hg19.fa
> >
> > hg19.fa.fai
>
> Can you put the 2bit file into the same folder?
>
> Cheers,
> Bjoern
>
>
> >
> > I’m using a torque setup.  A bam file is being used as input.  After
> > much trial and error I’ve been unable to figure out what I’m missing.
> >
> >  
> >
> > None of the solutions on google apply to my situation.
> >
> >  
> >
> > Has anyone else run into this configuration problem and solved it?
> >
> >  
> >
> > Thanks,
> >
> > -Sheldon
> >
> >  
> >
> > Sheldon Briand
> >
> > NRC Research Computing Support Analyst
> >
> > Research Computing Support / Soutien Informartique a la Recherche
> >
> > Operations, Science Portfolio / Operations, Portefeuil des sciences
> >
> > SSC-NRC / SPC-CNRC
> >
> > Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
> >
> > Halifax, NS  B3H 3Z1
> >
> > 902 426-1677
> >
> > [hidden email]
> >
> >  
> >
> >
> > ___________________________________________________________
> > 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:
> >   http://lists.bx.psu.edu/
> >
> > To search Galaxy mailing lists use the unified search at:
> >   http://galaxyproject.org/search/mailinglists/
>
>


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: GATK2

Briand, Sheldon

We do see hg19 in the reference genome box.  We are using revision 8bcc13094767 of the GATK2 wrapper.  The only line in the .loc file is the one listed in my first email.  I've put that line in both tool-data and tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/8bcc13094767 loc files. We didn't see the reference genome hg19 until the loc file for the repo was populated.

Thanks!
-Sheldon



-----Original Message-----
From: Björn Grüning [mailto:[hidden email]]
Sent: Thursday, January 30, 2014 1:33 PM
To: Briand, Sheldon
Cc: [hidden email]
Subject: Re: [galaxy-dev] GATK2

Hi Sheldon,

> The loc file is tabular.  I put the 2bit file in the directory and had no success.  Here is the rather lengthy commandline:
>
> #!/bin/sh
>
> export GALAXY_SLOTS_CONFIGURED="1"
> if [ -n "$SLURM_JOB_NUM_NODES" ]; then
>     GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"
> elif [ -n "$NSLOTS" ]; then
>     GALAXY_SLOTS="$NSLOTS"
> elif [ -f "$PBS_NODEFILE" ]; then
>     GALAXY_SLOTS=`wc -l < $PBS_NODEFILE` else
>     GALAXY_SLOTS="1"
>     unset GALAXY_SLOTS_CONFIGURED
> fi
>
> export GALAXY_SLOTS
> GALAXY_LIB="/software/packages/galaxy/galaxy-dist/lib"
> if [ "$GALAXY_LIB" != "None" ]; then
>     if [ -n "$PYTHONPATH" ]; then
>         PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
>     else
>         PYTHONPATH="$GALAXY_LIB"
>     fi
>     export PYTHONPATH
> fi
>
> [ -f "/home/galaxy/.bashrc" ] && . /home/galaxy/.bashrc cd
> /software/packages/galaxy/galaxy-dist/database/job_working_directory/0
> 00/101
> PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/samtoo
> ls/0.1.19/iuc/gatk2/8bcc13094767; export PACKA GE_BASE; .
> /software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc
> /gatk2/8bcc13094767/env.sh; PACKAGE
> _BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_s
> ettings/GATK2_PATH/iuc/gatk2/8bcc13094767; exp ort PACKAGE_BASE; .
> /software/packages/galaxy/galaxy-dist/dependancies/environment_setting
> s/GATK2_PATH/iuc/gatk2/8bc c13094767/env.sh;
> PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/enviro
> nment_settings/GATK2_SITE_OP TIONS/iuc/gatk2/8bcc13094767; export
> PACKAGE_BASE; .
> /software/packages/galaxy/galaxy-dist/dependancies/environment_
> settings/GATK2_SITE_OPTIONS/iuc/gatk2/8bcc13094767/env.sh; python /software/packages/galaxy/shed_tools/toolshed.g2.b
> x.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py     --stdout "/software/packages/galaxy/galaxy-dist/da
> tabase/files/000/dataset_126.dat"     -d "-I" "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_114.
> dat" "bam" "gatk_input"         -d "" "/software/packages/galaxy/galaxy-dist/database/files/_metadata_files/000/meta
> data_19.dat" "bam_index" "gatk_input"      -p '          java -jar "$GATK2_PATH/GenomeAnalysisTK.jar"        -T "Rea
> lignerTargetCreator"     -o "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_125.dat"      $GATK2_S
> ITE_OPTIONS      --num_cpu_threads_per_data_thread 1           --num_threads ${GALAXY_SLOTS:-4}            


>  -R ""

-> that is the error. Here needs to be your path to the fasta file. Can
you point to me to Tool Shed Version you are using and are you running the latest revision? Do you see hg19 / hg18 in the select-box under "using-reference genome"

Can you attach your gatk2_picard_index.loc?

Thanks,
Bjoern

>  
>  '; return_code=$?; cd /software/packages/galaxy/galaxy-dist;
> /software/packages/galaxy/galaxy-dist/set_metadata.sh
> ./database/files
> /software/packages/galaxy/galaxy-dist/database/job_working_directory/0
> 00/101 . /software/packages/g alaxy/galaxy-dist/universe_wsgi.ini
> /software/packages/galaxy/galaxy-dist/database/tmp/tmpfjJAKX
> /software/packages/
> galaxy/galaxy-dist/database/job_working_directory/000/101/galaxy.json
> /software/packages/galaxy/galaxy-dist/database
> /job_working_directory/000/101/metadata_in_HistoryDatasetAssociation_1
> 02_DXIvP5,/software/packages/galaxy/galaxy-dis
> t/database/job_working_directory/000/101/metadata_kwds_HistoryDatasetA
> ssociation_102_ifJAbu,/software/packages/galax
> y/galaxy-dist/database/job_working_directory/000/101/metadata_out_Hist
> oryDatasetAssociation_102_Ie2O0C,/software/pac
> kages/galaxy/galaxy-dist/database/job_working_directory/000/101/metada
> ta_results_HistoryDatasetAssociation_102_xLNtK
> a,,/software/packages/galaxy/galaxy-dist/database/job_working_director
> y/000/101/metadata_override_HistoryDatasetAsso
> ciation_102__IZJ7Y
> /software/packages/galaxy/galaxy-dist/database/job_working_directory/0
> 00/101/metadata_in_HistoryD
> atasetAssociation_103_uoVLce,/software/packages/galaxy/galaxy-dist/dat
> abase/job_working_directory/000/101/metadata_k
> wds_HistoryDatasetAssociation_103_1e5Jn2,/software/packages/galaxy/gal
> axy-dist/database/job_working_directory/000/10
> 1/metadata_out_HistoryDatasetAssociation_103_NNh80i,/software/packages
> /galaxy/galaxy-dist/database/job_working_direc
> tory/000/101/metadata_results_HistoryDatasetAssociation_103_ZVuezG,,/s
> oftware/packages/galaxy/galaxy-dist/database/j
> ob_working_directory/000/101/metadata_override_HistoryDatasetAssociation_103_LFaURY; sh -c "exit $return_code"
> echo $? > /software/packages/galaxy/galaxy-dist/database/pbs/101.ec
>
> Thanks,
> -Sheldon
>
> -----Original Message-----
> From: Björn Grüning [mailto:[hidden email]]
> Sent: Thursday, January 30, 2014 12:26 PM
> To: Briand, Sheldon
> Cc: [hidden email]
> Subject: Re: [galaxy-dev] GATK2
>
> Hi,
>
> do you have access to the generated commandline from Galaxy and can paste it her?
>
> >
> > I’ve installed the latest version (using GATK2.8-1) of the GATK2
> > wrapper here.  I’ve run into the following error:
> >
> > ##### ERROR MESSAGE: The fasta file you specified
> > (/tmp/tmp-gatk-V7IrBw) does not exist.
> >
> >  
> >
> > I see via much googling that this error is due to a user input
> > problem.  I’ve tried pointing the gatk2_picard_index.loc file in
> > tool-data to the proper data files:
> >
> > hg19 hg19    hg19    /software/packages/galaxy/data/picard/hg19.fa
>
> That look ok, as far as every token is separated by a tabular.
>
> >
> > where the following files exist:
> >
> > hg19.dict
> >
> > hg19.fa
> >
> > hg19.fa.fai
>
> Can you put the 2bit file into the same folder?
>
> Cheers,
> Bjoern
>
>
> >
> > I’m using a torque setup.  A bam file is being used as input.  After
> > much trial and error I’ve been unable to figure out what I’m missing.
> >
> >  
> >
> > None of the solutions on google apply to my situation.
> >
> >  
> >
> > Has anyone else run into this configuration problem and solved it?
> >
> >  
> >
> > Thanks,
> >
> > -Sheldon
> >
> >  
> >
> > Sheldon Briand
> >
> > NRC Research Computing Support Analyst
> >
> > Research Computing Support / Soutien Informartique a la Recherche
> >
> > Operations, Science Portfolio / Operations, Portefeuil des sciences
> >
> > SSC-NRC / SPC-CNRC
> >
> > Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
> >
> > Halifax, NS  B3H 3Z1
> >
> > 902 426-1677
> >
> > [hidden email]
> >
> >  
> >
> >
> > ___________________________________________________________
> > 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:
> >   http://lists.bx.psu.edu/
> >
> > To search Galaxy mailing lists use the unified search at:
> >   http://galaxyproject.org/search/mailinglists/
>
>



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: GATK2

Björn Grüning-3
I have no clue what is happening. Attached is my working *.loc flile.
See select-box is also filtered by the db-key of your dataset, but I think you habe hg19 as dbkey, otherwise you would not see the hg19 in the select box. There must be something wrong in you *.log file.


2014-01-30 Briand, Sheldon <[hidden email]>:

We do see hg19 in the reference genome box.  We are using revision 8bcc13094767 of the GATK2 wrapper.  The only line in the .loc file is the one listed in my first email.  I've put that line in both tool-data and tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/8bcc13094767 loc files. We didn't see the reference genome hg19 until the loc file for the repo was populated.

Thanks!
-Sheldon



-----Original Message-----
From: Björn Grüning [mailto:[hidden email]]
Sent: Thursday, January 30, 2014 1:33 PM
To: Briand, Sheldon
Cc: [hidden email]
Subject: Re: [galaxy-dev] GATK2

Hi Sheldon,

> The loc file is tabular.  I put the 2bit file in the directory and had no success.  Here is the rather lengthy commandline:
>
> #!/bin/sh
>
> export GALAXY_SLOTS_CONFIGURED="1"
> if [ -n "$SLURM_JOB_NUM_NODES" ]; then
>     GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"
> elif [ -n "$NSLOTS" ]; then
>     GALAXY_SLOTS="$NSLOTS"
> elif [ -f "$PBS_NODEFILE" ]; then
>     GALAXY_SLOTS=`wc -l < $PBS_NODEFILE` else
>     GALAXY_SLOTS="1"
>     unset GALAXY_SLOTS_CONFIGURED
> fi
>
> export GALAXY_SLOTS
> GALAXY_LIB="/software/packages/galaxy/galaxy-dist/lib"
> if [ "$GALAXY_LIB" != "None" ]; then
>     if [ -n "$PYTHONPATH" ]; then
>         PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
>     else
>         PYTHONPATH="$GALAXY_LIB"
>     fi
>     export PYTHONPATH
> fi
>
> [ -f "/home/galaxy/.bashrc" ] && . /home/galaxy/.bashrc cd
> /software/packages/galaxy/galaxy-dist/database/job_working_directory/0
> 00/101
> PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/samtoo
> ls/0.1.19/iuc/gatk2/8bcc13094767; export PACKA GE_BASE; .
> /software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc
> /gatk2/8bcc13094767/env.sh; PACKAGE
> _BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_s
> ettings/GATK2_PATH/iuc/gatk2/8bcc13094767; exp ort PACKAGE_BASE; .
> /software/packages/galaxy/galaxy-dist/dependancies/environment_setting
> s/GATK2_PATH/iuc/gatk2/8bc c13094767/env.sh;
> PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/enviro
> nment_settings/GATK2_SITE_OP TIONS/iuc/gatk2/8bcc13094767; export
> PACKAGE_BASE; .
> /software/packages/galaxy/galaxy-dist/dependancies/environment_
> settings/GATK2_SITE_OPTIONS/iuc/gatk2/8bcc13094767/env.sh; python /software/packages/galaxy/shed_tools/toolshed.g2.b
> x.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py     --stdout "/software/packages/galaxy/galaxy-dist/da
> tabase/files/000/dataset_126.dat"     -d "-I" "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_114.
> dat" "bam" "gatk_input"         -d "" "/software/packages/galaxy/galaxy-dist/database/files/_metadata_files/000/meta
> data_19.dat" "bam_index" "gatk_input"      -p '          java -jar "$GATK2_PATH/GenomeAnalysisTK.jar"        -T "Rea
> lignerTargetCreator"     -o "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_125.dat"      $GATK2_S
> ITE_OPTIONS      --num_cpu_threads_per_data_thread 1           --num_threads ${GALAXY_SLOTS:-4}


>  -R ""

-> that is the error. Here needs to be your path to the fasta file. Can
you point to me to Tool Shed Version you are using and are you running the latest revision? Do you see hg19 / hg18 in the select-box under "using-reference genome"

Can you attach your gatk2_picard_index.loc?

Thanks,
Bjoern

>
>  '; return_code=$?; cd /software/packages/galaxy/galaxy-dist;
> /software/packages/galaxy/galaxy-dist/set_metadata.sh
> ./database/files
> /software/packages/galaxy/galaxy-dist/database/job_working_directory/0
> 00/101 . /software/packages/g alaxy/galaxy-dist/universe_wsgi.ini
> /software/packages/galaxy/galaxy-dist/database/tmp/tmpfjJAKX
> /software/packages/
> galaxy/galaxy-dist/database/job_working_directory/000/101/galaxy.json
> /software/packages/galaxy/galaxy-dist/database
> /job_working_directory/000/101/metadata_in_HistoryDatasetAssociation_1
> 02_DXIvP5,/software/packages/galaxy/galaxy-dis
> t/database/job_working_directory/000/101/metadata_kwds_HistoryDatasetA
> ssociation_102_ifJAbu,/software/packages/galax
> y/galaxy-dist/database/job_working_directory/000/101/metadata_out_Hist
> oryDatasetAssociation_102_Ie2O0C,/software/pac
> kages/galaxy/galaxy-dist/database/job_working_directory/000/101/metada
> ta_results_HistoryDatasetAssociation_102_xLNtK
> a,,/software/packages/galaxy/galaxy-dist/database/job_working_director
> y/000/101/metadata_override_HistoryDatasetAsso
> ciation_102__IZJ7Y
> /software/packages/galaxy/galaxy-dist/database/job_working_directory/0
> 00/101/metadata_in_HistoryD
> atasetAssociation_103_uoVLce,/software/packages/galaxy/galaxy-dist/dat
> abase/job_working_directory/000/101/metadata_k
> wds_HistoryDatasetAssociation_103_1e5Jn2,/software/packages/galaxy/gal
> axy-dist/database/job_working_directory/000/10
> 1/metadata_out_HistoryDatasetAssociation_103_NNh80i,/software/packages
> /galaxy/galaxy-dist/database/job_working_direc
> tory/000/101/metadata_results_HistoryDatasetAssociation_103_ZVuezG,,/s
> oftware/packages/galaxy/galaxy-dist/database/j
> ob_working_directory/000/101/metadata_override_HistoryDatasetAssociation_103_LFaURY; sh -c "exit $return_code"
> echo $? > /software/packages/galaxy/galaxy-dist/database/pbs/101.ec
>
> Thanks,
> -Sheldon
>
> -----Original Message-----
> From: Björn Grüning [mailto:[hidden email]]
> Sent: Thursday, January 30, 2014 12:26 PM
> To: Briand, Sheldon
> Cc: [hidden email]
> Subject: Re: [galaxy-dev] GATK2
>
> Hi,
>
> do you have access to the generated commandline from Galaxy and can paste it her?
>
> >
> > I’ve installed the latest version (using GATK2.8-1) of the GATK2
> > wrapper here.  I’ve run into the following error:
> >
> > ##### ERROR MESSAGE: The fasta file you specified
> > (/tmp/tmp-gatk-V7IrBw) does not exist.
> >
> >
> >
> > I see via much googling that this error is due to a user input
> > problem.  I’ve tried pointing the gatk2_picard_index.loc file in
> > tool-data to the proper data files:
> >
> > hg19 hg19    hg19    /software/packages/galaxy/data/picard/hg19.fa
>
> That look ok, as far as every token is separated by a tabular.
>
> >
> > where the following files exist:
> >
> > hg19.dict
> >
> > hg19.fa
> >
> > hg19.fa.fai
>
> Can you put the 2bit file into the same folder?
>
> Cheers,
> Bjoern
>
>
> >
> > I’m using a torque setup.  A bam file is being used as input.  After
> > much trial and error I’ve been unable to figure out what I’m missing.
> >
> >
> >
> > None of the solutions on google apply to my situation.
> >
> >
> >
> > Has anyone else run into this configuration problem and solved it?
> >
> >
> >
> > Thanks,
> >
> > -Sheldon
> >
> >
> >
> > Sheldon Briand
> >
> > NRC Research Computing Support Analyst
> >
> > Research Computing Support / Soutien Informartique a la Recherche
> >
> > Operations, Science Portfolio / Operations, Portefeuil des sciences
> >
> > SSC-NRC / SPC-CNRC
> >
> > Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
> >
> > Halifax, NS  B3H 3Z1
> >
> > 902 426-1677
> >
> > [hidden email]
> >
> >
> >
> >
> > ___________________________________________________________
> > 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:
> >   http://lists.bx.psu.edu/
> >
> > To search Galaxy mailing lists use the unified search at:
> >   http://galaxyproject.org/search/mailinglists/
>
>




___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Open this post in threaded view
|

Re: GATK2

Briand, Sheldon

Hi,

 

Thanks for your help.  It turns out an extra carriage return snuck into the end of the .loc file.  Once I removed that everything worked.

 

-Sheldon

 

From: [hidden email] [mailto:[hidden email]]
Sent: Thursday, January 30, 2014 2:05 PM
To: Briand, Sheldon
Cc: [hidden email]
Subject: Re: [galaxy-dev] GATK2

 

I have no clue what is happening. Attached is my working *.loc flile.

See select-box is also filtered by the db-key of your dataset, but I think you habe hg19 as dbkey, otherwise you would not see the hg19 in the select box. There must be something wrong in you *.log file.

 

2014-01-30 Briand, Sheldon <[hidden email]>:


We do see hg19 in the reference genome box.  We are using revision 8bcc13094767 of the GATK2 wrapper.  The only line in the .loc file is the one listed in my first email.  I've put that line in both tool-data and tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/8bcc13094767 loc files. We didn't see the reference genome hg19 until the loc file for the repo was populated.

Thanks!

-Sheldon



-----Original Message-----
From: Björn Grüning [mailto:[hidden email]]

Sent: Thursday, January 30, 2014 1:33 PM
To: Briand, Sheldon
Cc: [hidden email]
Subject: Re: [galaxy-dev] GATK2

Hi Sheldon,


> The loc file is tabular.  I put the 2bit file in the directory and had no success.  Here is the rather lengthy commandline:
>
> #!/bin/sh
>
> export GALAXY_SLOTS_CONFIGURED="1"
> if [ -n "$SLURM_JOB_NUM_NODES" ]; then
>     GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"
> elif [ -n "$NSLOTS" ]; then
>     GALAXY_SLOTS="$NSLOTS"
> elif [ -f "$PBS_NODEFILE" ]; then
>     GALAXY_SLOTS=`wc -l < $PBS_NODEFILE` else
>     GALAXY_SLOTS="1"
>     unset GALAXY_SLOTS_CONFIGURED
> fi
>
> export GALAXY_SLOTS
> GALAXY_LIB="/software/packages/galaxy/galaxy-dist/lib"
> if [ "$GALAXY_LIB" != "None" ]; then
>     if [ -n "$PYTHONPATH" ]; then
>         PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
>     else
>         PYTHONPATH="$GALAXY_LIB"
>     fi
>     export PYTHONPATH
> fi
>
> [ -f "/home/galaxy/.bashrc" ] && . /home/galaxy/.bashrc cd
> /software/packages/galaxy/galaxy-dist/database/job_working_directory/0
> 00/101
> PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/samtoo
> ls/0.1.19/iuc/gatk2/8bcc13094767; export PACKA GE_BASE; .
> /software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc
> /gatk2/8bcc13094767/env.sh; PACKAGE
> _BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_s
> ettings/GATK2_PATH/iuc/gatk2/8bcc13094767; exp ort PACKAGE_BASE; .
> /software/packages/galaxy/galaxy-dist/dependancies/environment_setting
> s/GATK2_PATH/iuc/gatk2/8bc c13094767/env.sh;
> PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/enviro

> nment_settings/GATK2_SITE_OP TIONS/iuc/gatk2/8bcc13094767; export

> PACKAGE_BASE; .
> /software/packages/galaxy/galaxy-dist/dependancies/environment_
> settings/GATK2_SITE_OPTIONS/iuc/gatk2/8bcc13094767/env.sh; python /software/packages/galaxy/shed_tools/toolshed.g2.b
> x.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py     --stdout "/software/packages/galaxy/galaxy-dist/da
> tabase/files/000/dataset_126.dat"     -d "-I" "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_114.
> dat" "bam" "gatk_input"         -d "" "/software/packages/galaxy/galaxy-dist/database/files/_metadata_files/000/meta
> data_19.dat" "bam_index" "gatk_input"      -p '          java -jar "$GATK2_PATH/GenomeAnalysisTK.jar"        -T "Rea
> lignerTargetCreator"     -o "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_125.dat"      $GATK2_S
> ITE_OPTIONS      --num_cpu_threads_per_data_thread 1           --num_threads ${GALAXY_SLOTS:-4}



>  -R ""

-> that is the error. Here needs to be your path to the fasta file. Can
you point to me to Tool Shed Version you are using and are you running the latest revision? Do you see hg19 / hg18 in the select-box under "using-reference genome"

Can you attach your gatk2_picard_index.loc?

Thanks,
Bjoern

>
>  '; return_code=$?; cd /software/packages/galaxy/galaxy-dist;
> /software/packages/galaxy/galaxy-dist/set_metadata.sh
> ./database/files
> /software/packages/galaxy/galaxy-dist/database/job_working_directory/0
> 00/101 . /software/packages/g alaxy/galaxy-dist/universe_wsgi.ini
> /software/packages/galaxy/galaxy-dist/database/tmp/tmpfjJAKX
> /software/packages/
> galaxy/galaxy-dist/database/job_working_directory/000/101/galaxy.json
> /software/packages/galaxy/galaxy-dist/database
> /job_working_directory/000/101/metadata_in_HistoryDatasetAssociation_1
> 02_DXIvP5,/software/packages/galaxy/galaxy-dis
> t/database/job_working_directory/000/101/metadata_kwds_HistoryDatasetA
> ssociation_102_ifJAbu,/software/packages/galax
> y/galaxy-dist/database/job_working_directory/000/101/metadata_out_Hist
> oryDatasetAssociation_102_Ie2O0C,/software/pac
> kages/galaxy/galaxy-dist/database/job_working_directory/000/101/metada
> ta_results_HistoryDatasetAssociation_102_xLNtK
> a,,/software/packages/galaxy/galaxy-dist/database/job_working_director
> y/000/101/metadata_override_HistoryDatasetAsso
> ciation_102__IZJ7Y
> /software/packages/galaxy/galaxy-dist/database/job_working_directory/0
> 00/101/metadata_in_HistoryD
> atasetAssociation_103_uoVLce,/software/packages/galaxy/galaxy-dist/dat
> abase/job_working_directory/000/101/metadata_k
> wds_HistoryDatasetAssociation_103_1e5Jn2,/software/packages/galaxy/gal
> axy-dist/database/job_working_directory/000/10
> 1/metadata_out_HistoryDatasetAssociation_103_NNh80i,/software/packages
> /galaxy/galaxy-dist/database/job_working_direc
> tory/000/101/metadata_results_HistoryDatasetAssociation_103_ZVuezG,,/s
> oftware/packages/galaxy/galaxy-dist/database/j
> ob_working_directory/000/101/metadata_override_HistoryDatasetAssociation_103_LFaURY; sh -c "exit $return_code"
> echo $? > /software/packages/galaxy/galaxy-dist/database/pbs/101.ec
>
> Thanks,
> -Sheldon
>
> -----Original Message-----
> From: Björn Grüning [mailto:[hidden email]]
> Sent: Thursday, January 30, 2014 12:26 PM
> To: Briand, Sheldon
> Cc: [hidden email]
> Subject: Re: [galaxy-dev] GATK2
>
> Hi,
>
> do you have access to the generated commandline from Galaxy and can paste it her?
>
> >
> > I’ve installed the latest version (using GATK2.8-1) of the GATK2
> > wrapper here.  I’ve run into the following error:
> >
> > ##### ERROR MESSAGE: The fasta file you specified
> > (/tmp/tmp-gatk-V7IrBw) does not exist.
> >
> >
> >
> > I see via much googling that this error is due to a user input
> > problem.  I’ve tried pointing the gatk2_picard_index.loc file in
> > tool-data to the proper data files:
> >
> > hg19 hg19    hg19    /software/packages/galaxy/data/picard/hg19.fa
>
> That look ok, as far as every token is separated by a tabular.
>
> >
> > where the following files exist:
> >
> > hg19.dict
> >
> > hg19.fa
> >
> > hg19.fa.fai
>
> Can you put the 2bit file into the same folder?
>
> Cheers,
> Bjoern
>
>
> >
> > I’m using a torque setup.  A bam file is being used as input.  After
> > much trial and error I’ve been unable to figure out what I’m missing.
> >
> >
> >
> > None of the solutions on google apply to my situation.
> >
> >
> >
> > Has anyone else run into this configuration problem and solved it?
> >
> >
> >
> > Thanks,
> >
> > -Sheldon
> >
> >
> >
> > Sheldon Briand
> >
> > NRC Research Computing Support Analyst
> >
> > Research Computing Support / Soutien Informartique a la Recherche
> >
> > Operations, Science Portfolio / Operations, Portefeuil des sciences
> >
> > SSC-NRC / SPC-CNRC
> >
> > Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
> >
> > Halifax, NS  B3H 3Z1
> >
> > 902 426-1677
> >
> > [hidden email]
> >
> >
> >
> >
> > ___________________________________________________________
> > 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:
> >   http://lists.bx.psu.edu/
> >
> > To search Galaxy mailing lists use the unified search at:
> >   http://galaxyproject.org/search/mailinglists/
>
>

 


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