Toolshed partial installation ? deeptools error

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Toolshed partial installation ? deeptools error

juliech
Hi dev team,

I have a very big problem since I updated to galaxy 17.05 with
deeptools from toolshed.

Due to a bug in galaxy 17.05 with toolshed installed tools (reported
in this issue https://github.com/galaxyproject/galaxy/issues/4591), I
re-installed deeptools to try to resolve it.
Not resolved really but it's another problem. I temporarly bypassed it.

Here is my problem : I've installed deeptools from toolshed and when
we try to use "compute matrix" for example, we have this error message
:

Fatal error: Exit code 1 ()
Traceback (most recent call last):
  File "/usr/local/bin/computeMatrix", line 4, in <module>
    from deeptools.computeMatrix import main
ImportError: No module named deeptools.computeMatrix

It seems that wrapper are installed but not the tool "deeptools".

For more information, here it's the way for the installation :
search and install via toolshed
Install "suite_deeptools" (version 2.5.1.1.0 : 3d68b716965a)
Info in Manage tool dependencies : version=2.5.1, resolver=Conda,
green check symbol in the line with a list of all deeptools.

Galaxy 17.05, commit cfabe37 (21 sept 2017)

I've tried to uninstall/reinstall dependencies with conda but without success.

Have you any idea to install the deeptools please ?

Thanks.
Julie
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Re: Toolshed partial installation ? deeptools error

Von Kuster, Greg
This looks like the issue I’ve recently seen as well - I just discussed this with @bgruening on gitter - https://gitter.im/galaxy-iuc/iuc.  I’m using a work-around of creating the __deeptools conda env manually.  In my case, I’m not installing the whole suite, just the bamCoverage tool from the TS - https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_bam_coverage/5d11599b8a7d.  My work-around is to create the conda env manually:

$conda create -n __deeptools@2.5.1 deep tools=2.5.1

This env is created in the conda environment outside of Galaxy, so I just copy it to the conda environment I’ve configured for Galaxy.  This works, but it seems there is some issue with the installation from the TS, so perhaps a more ling term fix is needed.


On Oct 2, 2017, at 8:59 AM, julie dubois <[hidden email]> wrote:

Hi dev team,

I have a very big problem since I updated to galaxy 17.05 with
deeptools from toolshed.

Due to a bug in galaxy 17.05 with toolshed installed tools (reported
in this issue https://github.com/galaxyproject/galaxy/issues/4591), I
re-installed deeptools to try to resolve it.
Not resolved really but it's another problem. I temporarly bypassed it.

Here is my problem : I've installed deeptools from toolshed and when
we try to use "compute matrix" for example, we have this error message
:

Fatal error: Exit code 1 ()
Traceback (most recent call last):
 File "/usr/local/bin/computeMatrix", line 4, in <module>
   from deeptools.computeMatrix import main
ImportError: No module named deeptools.computeMatrix

It seems that wrapper are installed but not the tool "deeptools".

For more information, here it's the way for the installation :
search and install via toolshed
Install "suite_deeptools" (version 2.5.1.1.0 : 3d68b716965a)
Info in Manage tool dependencies : version=2.5.1, resolver=Conda,
green check symbol in the line with a list of all deeptools.

Galaxy 17.05, commit cfabe37 (21 sept 2017)

I've tried to uninstall/reinstall dependencies with conda but without success.

Have you any idea to install the deeptools please ?

Thanks.
Julie
___________________________________________________________
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in your mail client.  To manage your subscriptions to this
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Re: Toolshed partial installation ? deeptools error

juliech
Dear Greg,
I read your discussion with @bgruening and I think it's not exactly
the same. Because in my case, The executable IS present in my
galaxy-dist/tool_dependency/_conda/envs/__deeptools@2.5.1/bin .
The problem is far away in the execution when the tool (computeMatrix
in my example) try to load the python module deeptools.computeMatrix.
So is there a solution to discover where is the problem ?

Thanks

2017-10-02 15:16 GMT+02:00 Von Kuster, Greg <[hidden email]>:

> This looks like the issue I’ve recently seen as well - I just discussed this
> with @bgruening on gitter - https://gitter.im/galaxy-iuc/iuc.  I’m using a
> work-around of creating the __deeptools conda env manually.  In my case, I’m
> not installing the whole suite, just the bamCoverage tool from the TS -
> https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_bam_coverage/5d11599b8a7d.
> My work-around is to create the conda env manually:
>
> $conda create -n __deeptools@2.5.1 deep tools=2.5.1
>
> This env is created in the conda environment outside of Galaxy, so I just
> copy it to the conda environment I’ve configured for Galaxy.  This works,
> but it seems there is some issue with the installation from the TS, so
> perhaps a more ling term fix is needed.
>
>
> On Oct 2, 2017, at 8:59 AM, julie dubois <[hidden email]> wrote:
>
> Hi dev team,
>
> I have a very big problem since I updated to galaxy 17.05 with
> deeptools from toolshed.
>
> Due to a bug in galaxy 17.05 with toolshed installed tools (reported
> in this issue https://github.com/galaxyproject/galaxy/issues/4591), I
> re-installed deeptools to try to resolve it.
> Not resolved really but it's another problem. I temporarly bypassed it.
>
> Here is my problem : I've installed deeptools from toolshed and when
> we try to use "compute matrix" for example, we have this error message
> :
>
> Fatal error: Exit code 1 ()
> Traceback (most recent call last):
>  File "/usr/local/bin/computeMatrix", line 4, in <module>
>    from deeptools.computeMatrix import main
> ImportError: No module named deeptools.computeMatrix
>
> It seems that wrapper are installed but not the tool "deeptools".
>
> For more information, here it's the way for the installation :
> search and install via toolshed
> Install "suite_deeptools" (version 2.5.1.1.0 : 3d68b716965a)
> Info in Manage tool dependencies : version=2.5.1, resolver=Conda,
> green check symbol in the line with a list of all deeptools.
>
> Galaxy 17.05, commit cfabe37 (21 sept 2017)
>
> I've tried to uninstall/reinstall dependencies with conda but without
> success.
>
> Have you any idea to install the deeptools please ?
>
> Thanks.
> Julie
> ___________________________________________________________
> 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/
>
>
___________________________________________________________
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: Toolshed partial installation ? deeptools error

Marius van den Beek
Hi Julie, 

any chance you are setting PYTHONPATH before starting galaxy's job handlers (a common place would the supervisor config, in case you're using that)?
This will interfere with all python modules that are installed via conda.

Best,
Marius

On 3 October 2017 at 09:13, julie dubois <[hidden email]> wrote:
Dear Greg,
I read your discussion with @bgruening and I think it's not exactly
the same. Because in my case, The executable IS present in my
galaxy-dist/tool_dependency/_conda/envs/__deeptools@2.5.1/bin .
The problem is far away in the execution when the tool (computeMatrix
in my example) try to load the python module deeptools.computeMatrix.
So is there a solution to discover where is the problem ?

Thanks

2017-10-02 15:16 GMT+02:00 Von Kuster, Greg <[hidden email]>:
> This looks like the issue I’ve recently seen as well - I just discussed this
> with @bgruening on gitter - https://gitter.im/galaxy-iuc/iuc.  I’m using a
> work-around of creating the __deeptools conda env manually.  In my case, I’m
> not installing the whole suite, just the bamCoverage tool from the TS -
> https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_bam_coverage/5d11599b8a7d.
> My work-around is to create the conda env manually:
>
> $conda create -n __deeptools@2.5.1 deep tools=2.5.1
>
> This env is created in the conda environment outside of Galaxy, so I just
> copy it to the conda environment I’ve configured for Galaxy.  This works,
> but it seems there is some issue with the installation from the TS, so
> perhaps a more ling term fix is needed.
>
>
> On Oct 2, 2017, at 8:59 AM, julie dubois <[hidden email]> wrote:
>
> Hi dev team,
>
> I have a very big problem since I updated to galaxy 17.05 with
> deeptools from toolshed.
>
> Due to a bug in galaxy 17.05 with toolshed installed tools (reported
> in this issue https://github.com/galaxyproject/galaxy/issues/4591), I
> re-installed deeptools to try to resolve it.
> Not resolved really but it's another problem. I temporarly bypassed it.
>
> Here is my problem : I've installed deeptools from toolshed and when
> we try to use "compute matrix" for example, we have this error message
> :
>
> Fatal error: Exit code 1 ()
> Traceback (most recent call last):
>  File "/usr/local/bin/computeMatrix", line 4, in <module>
>    from deeptools.computeMatrix import main
> ImportError: No module named deeptools.computeMatrix
>
> It seems that wrapper are installed but not the tool "deeptools".
>
> For more information, here it's the way for the installation :
> search and install via toolshed
> Install "suite_deeptools" (version 2.5.1.1.0 : 3d68b716965a)
> Info in Manage tool dependencies : version=2.5.1, resolver=Conda,
> green check symbol in the line with a list of all deeptools.
>
> Galaxy 17.05, commit cfabe37 (21 sept 2017)
>
> I've tried to uninstall/reinstall dependencies with conda but without
> success.
>
> Have you any idea to install the deeptools please ?
>
> Thanks.
> Julie
> ___________________________________________________________
> 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/
>
>
___________________________________________________________
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:
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To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/


___________________________________________________________
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in your mail client.  To manage your subscriptions to this
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Re: Toolshed partial installation ? deeptools error

Marius van den Beek
Also upon re-reading I see that your dependency is being picked up from /usr/local/bin,
which indicates that this isn't using conda at all. 
A small excerpt from the logs when you try to run the tool may be helpful
to understand what is going on there.

Best,
Marius

On 3 October 2017 at 09:29, Marius van den Beek <[hidden email]> wrote:
Hi Julie, 

any chance you are setting PYTHONPATH before starting galaxy's job handlers (a common place would the supervisor config, in case you're using that)?
This will interfere with all python modules that are installed via conda.

Best,
Marius

On 3 October 2017 at 09:13, julie dubois <[hidden email]> wrote:
Dear Greg,
I read your discussion with @bgruening and I think it's not exactly
the same. Because in my case, The executable IS present in my
galaxy-dist/tool_dependency/_conda/envs/__deeptools@2.5.1/bin .
The problem is far away in the execution when the tool (computeMatrix
in my example) try to load the python module deeptools.computeMatrix.
So is there a solution to discover where is the problem ?

Thanks

2017-10-02 15:16 GMT+02:00 Von Kuster, Greg <[hidden email]>:
> This looks like the issue I’ve recently seen as well - I just discussed this
> with @bgruening on gitter - https://gitter.im/galaxy-iuc/iuc.  I’m using a
> work-around of creating the __deeptools conda env manually.  In my case, I’m
> not installing the whole suite, just the bamCoverage tool from the TS -
> https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_bam_coverage/5d11599b8a7d.
> My work-around is to create the conda env manually:
>
> $conda create -n __deeptools@2.5.1 deep tools=2.5.1
>
> This env is created in the conda environment outside of Galaxy, so I just
> copy it to the conda environment I’ve configured for Galaxy.  This works,
> but it seems there is some issue with the installation from the TS, so
> perhaps a more ling term fix is needed.
>
>
> On Oct 2, 2017, at 8:59 AM, julie dubois <[hidden email]> wrote:
>
> Hi dev team,
>
> I have a very big problem since I updated to galaxy 17.05 with
> deeptools from toolshed.
>
> Due to a bug in galaxy 17.05 with toolshed installed tools (reported
> in this issue https://github.com/galaxyproject/galaxy/issues/4591), I
> re-installed deeptools to try to resolve it.
> Not resolved really but it's another problem. I temporarly bypassed it.
>
> Here is my problem : I've installed deeptools from toolshed and when
> we try to use "compute matrix" for example, we have this error message
> :
>
> Fatal error: Exit code 1 ()
> Traceback (most recent call last):
>  File "/usr/local/bin/computeMatrix", line 4, in <module>
>    from deeptools.computeMatrix import main
> ImportError: No module named deeptools.computeMatrix
>
> It seems that wrapper are installed but not the tool "deeptools".
>
> For more information, here it's the way for the installation :
> search and install via toolshed
> Install "suite_deeptools" (version 2.5.1.1.0 : 3d68b716965a)
> Info in Manage tool dependencies : version=2.5.1, resolver=Conda,
> green check symbol in the line with a list of all deeptools.
>
> Galaxy 17.05, commit cfabe37 (21 sept 2017)
>
> I've tried to uninstall/reinstall dependencies with conda but without
> success.
>
> Have you any idea to install the deeptools please ?
>
> Thanks.
> Julie
> ___________________________________________________________
> 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/
>
>
___________________________________________________________
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:
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Re: Toolshed partial installation ? deeptools error

juliech
When I run computeMatrix, I have on ly this in the log file :

192.168.000.000 - - [03/oct./2017:10:16:07 +0200] "POST
/galaxy/api/tools/deeptools_compute_matrix/build HTTP/1.1" 200 -
"http://192.168.100.000:8080/galaxy?job_id=7e6a9fe53e29fc38&__identifer=tmmenbexqep"
"Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:37.0) Gecko/20100101
Firefox/37.0"

 On the job working directory I have this in tool_script.sh :
 #!/bin/bash

# The following block can be used by the job system
# to ensure this script is runnable before actually attempting
# to run it.
if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
    exit 42
fi
export PATH=$PATH:'/data/galaxy-dist/tool_dependency/_conda/envs/__deeptools@2.5.1/bin'
; computeMatrix --version >
/data/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_38413 2>&1; ln -f
-s "/data/galaxy-dist/database/files/080/dataset_80817.dat"
"MACS2narrow_SamToBam_Bowtie_mapped_readsTrim__0.bw" &&    ln -f -s
"/data/galaxy-dist/database/files/080/dataset_80593.dat"
"MACS2narrow_SamToBam_Bowtie_mapped_readsTrim__0.bed" &&
computeMatrix  scale-regions --regionsFileName
'MACS2narrow_SamToBam_Bowtie_mapped_readsTrim__0.bed'  --scoreFileName
'MACS2narrow_SamToBam_Bowtie_mapped_readsTrim__0.bw'  --outFileName
'/data/galaxy-dist/database/files/080/dataset_80995.dat'
--numberOfProcessors "${GALAXY_SLOTS:-4}"   --regionBodyLength 500

It seems to export the good path for executable. So I don't understand.

In the galaxy_38413.sh :
#!/bin/bash



# The following block can be used by the job system
# to ensure this script is runnable before actually attempting
# to run it.
if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
    exit 42
fi

GALAXY_SLOTS="1"; export GALAXY_SLOTS;
export GALAXY_SLOTS
PRESERVE_GALAXY_ENVIRONMENT="True"
GALAXY_LIB="/data/galaxy-dist/lib"
if [ "$GALAXY_LIB" != "None" -a "$PRESERVE_GALAXY_ENVIRONMENT" = "True" ]; then
    if [ -n "$PYTHONPATH" ]; then
        PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
    else
        PYTHONPATH="$GALAXY_LIB"
    fi
    export PYTHONPATH
fi

GALAXY_VIRTUAL_ENV="/data/galaxy-dist/.venv"
if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" \
     -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" -a
"$PRESERVE_GALAXY_ENVIRONMENT" = "True" ]; then
    . "$GALAXY_VIRTUAL_ENV/bin/activate"
fi
echo "$GALAXY_SLOTS" >
'/data/galaxy-dist/database/job_working_directory/038/38413/__instrument_core_galaxy_slots'
date +"%s" > /data/galaxy-dist/database/job_working_directory/038/38413/__instrument_core_epoch_start
cd /data/galaxy-dist/database/job_working_directory/038/38413
rm -rf working; mkdir -p working; cd working;
/data/galaxy-dist/database/job_working_directory/038/38413/tool_script.sh;
return_code=$?; cd
'/data/galaxy-dist/database/job_working_directory/038/38413';
if [ "$GALAXY_LIB" != "None" ]; then
    if [ -n "$PYTHONPATH" ]; then
        PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
    else
        PYTHONPATH="$GALAXY_LIB"
    fi
    export PYTHONPATH
fi
if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV"      -a -f
"$GALAXY_VIRTUAL_ENV/bin/activate" ]; then
    . "$GALAXY_VIRTUAL_ENV/bin/activate"
fi
GALAXY_PYTHON=`command -v python`
export PATH=$PATH:'/data/galaxy-dist/tool_dependency/_conda/envs/__samtools@1.3.1/bin'
; python "/data/galaxy-dist/database/job_working_directory/038/38413/set_metadata_c9AkjG.py"
"/data/galaxy-dist/database/job_working_directory/038/38413/registry.xml"
"/data/galaxy-dist/database/job_working_directory/038/38413/working/galaxy.json"
"/data/galaxy-dist/database/job_working_directory/038/38413/metadata_in_HistoryDatasetAssociation_72822_Eqsgna,/data/galaxy-dist/database/job_working_directory/038/38413/metadata_kwds_HistoryDatasetAssociation_72822_3VQ3be,/data/galaxy-dist/database/job_working_directory/038/38413/metadata_out_HistoryDatasetAssociation_72822_TQg8Pq,/data/galaxy-dist/database/job_working_directory/038/38413/metadata_results_HistoryDatasetAssociation_72822_ctopJa,/data/galaxy-dist/database/files/080/dataset_80995.dat,/data/galaxy-dist/database/job_working_directory/038/38413/metadata_override_HistoryDatasetAssociation_72822_Izp4CZ"
5242880; sh -c "exit $return_code"
echo $? > /data/galaxy-dist/database/job_working_directory/038/38413/galaxy_38413.ec
date +"%s" > /data/galaxy-dist/database/job_working_directory/038/38413/__instrument_core_epoch_end


May be my galaxy.ini in not well configured for conda.
For the moment concerning conda in galaxy.ini, I have these lines uncommented :

preserve_python_environment = legacy_and_local
dependency_resolvers_config_file = config/dependency_resolvers_conf.xml



2017-10-03 9:53 GMT+02:00 Marius van den Beek <[hidden email]>:

> Also upon re-reading I see that your dependency is being picked up from
> /usr/local/bin,
> which indicates that this isn't using conda at all.
> A small excerpt from the logs when you try to run the tool may be helpful
> to understand what is going on there.
>
> Best,
> Marius
>
> On 3 October 2017 at 09:29, Marius van den Beek <[hidden email]>
> wrote:
>>
>> Hi Julie,
>>
>> any chance you are setting PYTHONPATH before starting galaxy's job
>> handlers (a common place would the supervisor config, in case you're using
>> that)?
>> This will interfere with all python modules that are installed via conda.
>>
>> Best,
>> Marius
>>
>> On 3 October 2017 at 09:13, julie dubois <[hidden email]> wrote:
>>>
>>> Dear Greg,
>>> I read your discussion with @bgruening and I think it's not exactly
>>> the same. Because in my case, The executable IS present in my
>>> galaxy-dist/tool_dependency/_conda/envs/__deeptools@2.5.1/bin .
>>> The problem is far away in the execution when the tool (computeMatrix
>>> in my example) try to load the python module deeptools.computeMatrix.
>>> So is there a solution to discover where is the problem ?
>>>
>>> Thanks
>>>
>>> 2017-10-02 15:16 GMT+02:00 Von Kuster, Greg <[hidden email]>:
>>> > This looks like the issue I’ve recently seen as well - I just discussed
>>> > this
>>> > with @bgruening on gitter - https://gitter.im/galaxy-iuc/iuc.  I’m
>>> > using a
>>> > work-around of creating the __deeptools conda env manually.  In my
>>> > case, I’m
>>> > not installing the whole suite, just the bamCoverage tool from the TS -
>>> >
>>> > https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_bam_coverage/5d11599b8a7d.
>>> > My work-around is to create the conda env manually:
>>> >
>>> > $conda create -n __deeptools@2.5.1 deep tools=2.5.1
>>> >
>>> > This env is created in the conda environment outside of Galaxy, so I
>>> > just
>>> > copy it to the conda environment I’ve configured for Galaxy.  This
>>> > works,
>>> > but it seems there is some issue with the installation from the TS, so
>>> > perhaps a more ling term fix is needed.
>>> >
>>> >
>>> > On Oct 2, 2017, at 8:59 AM, julie dubois <[hidden email]> wrote:
>>> >
>>> > Hi dev team,
>>> >
>>> > I have a very big problem since I updated to galaxy 17.05 with
>>> > deeptools from toolshed.
>>> >
>>> > Due to a bug in galaxy 17.05 with toolshed installed tools (reported
>>> > in this issue https://github.com/galaxyproject/galaxy/issues/4591), I
>>> > re-installed deeptools to try to resolve it.
>>> > Not resolved really but it's another problem. I temporarly bypassed it.
>>> >
>>> > Here is my problem : I've installed deeptools from toolshed and when
>>> > we try to use "compute matrix" for example, we have this error message
>>> > :
>>> >
>>> > Fatal error: Exit code 1 ()
>>> > Traceback (most recent call last):
>>> >  File "/usr/local/bin/computeMatrix", line 4, in <module>
>>> >    from deeptools.computeMatrix import main
>>> > ImportError: No module named deeptools.computeMatrix
>>> >
>>> > It seems that wrapper are installed but not the tool "deeptools".
>>> >
>>> > For more information, here it's the way for the installation :
>>> > search and install via toolshed
>>> > Install "suite_deeptools" (version 2.5.1.1.0 : 3d68b716965a)
>>> > Info in Manage tool dependencies : version=2.5.1, resolver=Conda,
>>> > green check symbol in the line with a list of all deeptools.
>>> >
>>> > Galaxy 17.05, commit cfabe37 (21 sept 2017)
>>> >
>>> > I've tried to uninstall/reinstall dependencies with conda but without
>>> > success.
>>> >
>>> > Have you any idea to install the deeptools please ?
>>> >
>>> > Thanks.
>>> > Julie
>>> > ___________________________________________________________
>>> > 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/
>>> >
>>> >
>>> ___________________________________________________________
>>> 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/
>>
>>
>
___________________________________________________________
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/

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Re: Toolshed partial installation ? deeptools error

Marius van den Beek
So the `preserve_python_environment = legacy_and_local` setting is causing this for you.
Now normally deeptools is not a local tool, but I understand that because of https://github.com/galaxyproject/galaxy/issues/4591,
you have manipulated the shed_tool_conf.xml file, and it is now being considered as a local tool.
In any case this setting should be set to legacy_and_local only if you experience difficulties when it is not set,
that is why `legacy` is the default.


On 3 October 2017 at 10:30, julie dubois <[hidden email]> wrote:
When I run computeMatrix, I have on ly this in the log file :

192.168.000.000 - - [03/oct./2017:10:16:07 +0200] "POST
/galaxy/api/tools/deeptools_compute_matrix/build HTTP/1.1" 200 -
"http://192.168.100.000:8080/galaxy?job_id=7e6a9fe53e29fc38&__identifer=tmmenbexqep"
"Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:37.0) Gecko/20100101
Firefox/37.0"

 On the job working directory I have this in tool_script.sh :
 #!/bin/bash

# The following block can be used by the job system
# to ensure this script is runnable before actually attempting
# to run it.
if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
    exit 42
fi
export PATH=$PATH:'/data/galaxy-dist/tool_dependency/_conda/envs/__deeptools@2.5.1/bin'
; computeMatrix --version >
/data/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_38413 2>&1; ln -f
-s "/data/galaxy-dist/database/files/080/dataset_80817.dat"
"MACS2narrow_SamToBam_Bowtie_mapped_readsTrim__0.bw" &&    ln -f -s
"/data/galaxy-dist/database/files/080/dataset_80593.dat"
"MACS2narrow_SamToBam_Bowtie_mapped_readsTrim__0.bed" &&
computeMatrix  scale-regions --regionsFileName
'MACS2narrow_SamToBam_Bowtie_mapped_readsTrim__0.bed'  --scoreFileName
'MACS2narrow_SamToBam_Bowtie_mapped_readsTrim__0.bw'  --outFileName
'/data/galaxy-dist/database/files/080/dataset_80995.dat'
--numberOfProcessors "${GALAXY_SLOTS:-4}"   --regionBodyLength 500

It seems to export the good path for executable. So I don't understand.

In the galaxy_38413.sh :
#!/bin/bash



# The following block can be used by the job system
# to ensure this script is runnable before actually attempting
# to run it.
if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
    exit 42
fi

GALAXY_SLOTS="1"; export GALAXY_SLOTS;
export GALAXY_SLOTS
PRESERVE_GALAXY_ENVIRONMENT="True"
GALAXY_LIB="/data/galaxy-dist/lib"
if [ "$GALAXY_LIB" != "None" -a "$PRESERVE_GALAXY_ENVIRONMENT" = "True" ]; then
    if [ -n "$PYTHONPATH" ]; then
        PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
    else
        PYTHONPATH="$GALAXY_LIB"
    fi
    export PYTHONPATH
fi

GALAXY_VIRTUAL_ENV="/data/galaxy-dist/.venv"
if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" \
     -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" -a
"$PRESERVE_GALAXY_ENVIRONMENT" = "True" ]; then
    . "$GALAXY_VIRTUAL_ENV/bin/activate"
fi
echo "$GALAXY_SLOTS" >
'/data/galaxy-dist/database/job_working_directory/038/38413/__instrument_core_galaxy_slots'
date +"%s" > /data/galaxy-dist/database/job_working_directory/038/38413/__instrument_core_epoch_start
cd /data/galaxy-dist/database/job_working_directory/038/38413
rm -rf working; mkdir -p working; cd working;
/data/galaxy-dist/database/job_working_directory/038/38413/tool_script.sh;
return_code=$?; cd
'/data/galaxy-dist/database/job_working_directory/038/38413';
if [ "$GALAXY_LIB" != "None" ]; then
    if [ -n "$PYTHONPATH" ]; then
        PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
    else
        PYTHONPATH="$GALAXY_LIB"
    fi
    export PYTHONPATH
fi
if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV"      -a -f
"$GALAXY_VIRTUAL_ENV/bin/activate" ]; then
    . "$GALAXY_VIRTUAL_ENV/bin/activate"
fi
GALAXY_PYTHON=`command -v python`
export PATH=$PATH:'/data/galaxy-dist/tool_dependency/_conda/envs/__samtools@1.3.1/bin'
; python "/data/galaxy-dist/database/job_working_directory/038/38413/set_metadata_c9AkjG.py"
"/data/galaxy-dist/database/job_working_directory/038/38413/registry.xml"
"/data/galaxy-dist/database/job_working_directory/038/38413/working/galaxy.json"
"/data/galaxy-dist/database/job_working_directory/038/38413/metadata_in_HistoryDatasetAssociation_72822_Eqsgna,/data/galaxy-dist/database/job_working_directory/038/38413/metadata_kwds_HistoryDatasetAssociation_72822_3VQ3be,/data/galaxy-dist/database/job_working_directory/038/38413/metadata_out_HistoryDatasetAssociation_72822_TQg8Pq,/data/galaxy-dist/database/job_working_directory/038/38413/metadata_results_HistoryDatasetAssociation_72822_ctopJa,/data/galaxy-dist/database/files/080/dataset_80995.dat,/data/galaxy-dist/database/job_working_directory/038/38413/metadata_override_HistoryDatasetAssociation_72822_Izp4CZ"
5242880; sh -c "exit $return_code"
echo $? > /data/galaxy-dist/database/job_working_directory/038/38413/galaxy_38413.ec
date +"%s" > /data/galaxy-dist/database/job_working_directory/038/38413/__instrument_core_epoch_end


May be my galaxy.ini in not well configured for conda.
For the moment concerning conda in galaxy.ini, I have these lines uncommented :

preserve_python_environment = legacy_and_local
dependency_resolvers_config_file = config/dependency_resolvers_conf.xml



2017-10-03 9:53 GMT+02:00 Marius van den Beek <[hidden email]>:
> Also upon re-reading I see that your dependency is being picked up from
> /usr/local/bin,
> which indicates that this isn't using conda at all.
> A small excerpt from the logs when you try to run the tool may be helpful
> to understand what is going on there.
>
> Best,
> Marius
>
> On 3 October 2017 at 09:29, Marius van den Beek <[hidden email]>
> wrote:
>>
>> Hi Julie,
>>
>> any chance you are setting PYTHONPATH before starting galaxy's job
>> handlers (a common place would the supervisor config, in case you're using
>> that)?
>> This will interfere with all python modules that are installed via conda.
>>
>> Best,
>> Marius
>>
>> On 3 October 2017 at 09:13, julie dubois <[hidden email]> wrote:
>>>
>>> Dear Greg,
>>> I read your discussion with @bgruening and I think it's not exactly
>>> the same. Because in my case, The executable IS present in my
>>> galaxy-dist/tool_dependency/_conda/envs/__deeptools@2.5.1/bin .
>>> The problem is far away in the execution when the tool (computeMatrix
>>> in my example) try to load the python module deeptools.computeMatrix.
>>> So is there a solution to discover where is the problem ?
>>>
>>> Thanks
>>>
>>> 2017-10-02 15:16 GMT+02:00 Von Kuster, Greg <[hidden email]>:
>>> > This looks like the issue I’ve recently seen as well - I just discussed
>>> > this
>>> > with @bgruening on gitter - https://gitter.im/galaxy-iuc/iuc.  I’m
>>> > using a
>>> > work-around of creating the __deeptools conda env manually.  In my
>>> > case, I’m
>>> > not installing the whole suite, just the bamCoverage tool from the TS -
>>> >
>>> > https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_bam_coverage/5d11599b8a7d.
>>> > My work-around is to create the conda env manually:
>>> >
>>> > $conda create -n __deeptools@2.5.1 deep tools=2.5.1
>>> >
>>> > This env is created in the conda environment outside of Galaxy, so I
>>> > just
>>> > copy it to the conda environment I’ve configured for Galaxy.  This
>>> > works,
>>> > but it seems there is some issue with the installation from the TS, so
>>> > perhaps a more ling term fix is needed.
>>> >
>>> >
>>> > On Oct 2, 2017, at 8:59 AM, julie dubois <[hidden email]> wrote:
>>> >
>>> > Hi dev team,
>>> >
>>> > I have a very big problem since I updated to galaxy 17.05 with
>>> > deeptools from toolshed.
>>> >
>>> > Due to a bug in galaxy 17.05 with toolshed installed tools (reported
>>> > in this issue https://github.com/galaxyproject/galaxy/issues/4591), I
>>> > re-installed deeptools to try to resolve it.
>>> > Not resolved really but it's another problem. I temporarly bypassed it.
>>> >
>>> > Here is my problem : I've installed deeptools from toolshed and when
>>> > we try to use "compute matrix" for example, we have this error message
>>> > :
>>> >
>>> > Fatal error: Exit code 1 ()
>>> > Traceback (most recent call last):
>>> >  File "/usr/local/bin/computeMatrix", line 4, in <module>
>>> >    from deeptools.computeMatrix import main
>>> > ImportError: No module named deeptools.computeMatrix
>>> >
>>> > It seems that wrapper are installed but not the tool "deeptools".
>>> >
>>> > For more information, here it's the way for the installation :
>>> > search and install via toolshed
>>> > Install "suite_deeptools" (version 2.5.1.1.0 : 3d68b716965a)
>>> > Info in Manage tool dependencies : version=2.5.1, resolver=Conda,
>>> > green check symbol in the line with a list of all deeptools.
>>> >
>>> > Galaxy 17.05, commit cfabe37 (21 sept 2017)
>>> >
>>> > I've tried to uninstall/reinstall dependencies with conda but without
>>> > success.
>>> >
>>> > Have you any idea to install the deeptools please ?
>>> >
>>> > Thanks.
>>> > Julie
>>> > ___________________________________________________________
>>> > 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/
>>> >
>>> >
>>> ___________________________________________________________
>>> 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/
>>
>>
>


___________________________________________________________
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/

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Re: Toolshed partial installation ? deeptools error

juliech
OK, so I've modified my galaxy.ini to set `preserve_python_environment= legacy`
Then I 'm going back to the good shed_tool_conf.xml file : it means no
modification in this file regarding the original.
I've restarted galaxy and the error traced in
https://github.com/galaxyproject/galaxy/issues/4591  reappears.
So, I'm answering you in
https://github.com/galaxyproject/galaxy/issues/4591 and may be the
problem here  will disappear.

Thanks again for your help

2017-10-03 10:41 GMT+02:00 Marius van den Beek <[hidden email]>:

> So the `preserve_python_environment = legacy_and_local` setting is causing
> this for you.
> Now normally deeptools is not a local tool, but I understand that because of
> https://github.com/galaxyproject/galaxy/issues/4591,
> you have manipulated the shed_tool_conf.xml file, and it is now being
> considered as a local tool.
> In any case this setting should be set to legacy_and_local only if you
> experience difficulties when it is not set,
> that is why `legacy` is the default.
>
>
> On 3 October 2017 at 10:30, julie dubois <[hidden email]> wrote:
>>
>> When I run computeMatrix, I have on ly this in the log file :
>>
>> 192.168.000.000 - - [03/oct./2017:10:16:07 +0200] "POST
>> /galaxy/api/tools/deeptools_compute_matrix/build HTTP/1.1" 200 -
>>
>> "http://192.168.100.000:8080/galaxy?job_id=7e6a9fe53e29fc38&__identifer=tmmenbexqep"
>> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:37.0) Gecko/20100101
>> Firefox/37.0"
>>
>>  On the job working directory I have this in tool_script.sh :
>>  #!/bin/bash
>>
>> # The following block can be used by the job system
>> # to ensure this script is runnable before actually attempting
>> # to run it.
>> if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
>>     exit 42
>> fi
>> export
>> PATH=$PATH:'/data/galaxy-dist/tool_dependency/_conda/envs/__deeptools@2.5.1/bin'
>> ; computeMatrix --version >
>> /data/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_38413 2>&1; ln -f
>> -s "/data/galaxy-dist/database/files/080/dataset_80817.dat"
>> "MACS2narrow_SamToBam_Bowtie_mapped_readsTrim__0.bw" &&    ln -f -s
>> "/data/galaxy-dist/database/files/080/dataset_80593.dat"
>> "MACS2narrow_SamToBam_Bowtie_mapped_readsTrim__0.bed" &&
>> computeMatrix  scale-regions --regionsFileName
>> 'MACS2narrow_SamToBam_Bowtie_mapped_readsTrim__0.bed'  --scoreFileName
>> 'MACS2narrow_SamToBam_Bowtie_mapped_readsTrim__0.bw'  --outFileName
>> '/data/galaxy-dist/database/files/080/dataset_80995.dat'
>> --numberOfProcessors "${GALAXY_SLOTS:-4}"   --regionBodyLength 500
>>
>> It seems to export the good path for executable. So I don't understand.
>>
>> In the galaxy_38413.sh :
>> #!/bin/bash
>>
>>
>>
>> # The following block can be used by the job system
>> # to ensure this script is runnable before actually attempting
>> # to run it.
>> if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
>>     exit 42
>> fi
>>
>> GALAXY_SLOTS="1"; export GALAXY_SLOTS;
>> export GALAXY_SLOTS
>> PRESERVE_GALAXY_ENVIRONMENT="True"
>> GALAXY_LIB="/data/galaxy-dist/lib"
>> if [ "$GALAXY_LIB" != "None" -a "$PRESERVE_GALAXY_ENVIRONMENT" = "True" ];
>> then
>>     if [ -n "$PYTHONPATH" ]; then
>>         PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
>>     else
>>         PYTHONPATH="$GALAXY_LIB"
>>     fi
>>     export PYTHONPATH
>> fi
>>
>> GALAXY_VIRTUAL_ENV="/data/galaxy-dist/.venv"
>> if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" \
>>      -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" -a
>> "$PRESERVE_GALAXY_ENVIRONMENT" = "True" ]; then
>>     . "$GALAXY_VIRTUAL_ENV/bin/activate"
>> fi
>> echo "$GALAXY_SLOTS" >
>>
>> '/data/galaxy-dist/database/job_working_directory/038/38413/__instrument_core_galaxy_slots'
>> date +"%s" >
>> /data/galaxy-dist/database/job_working_directory/038/38413/__instrument_core_epoch_start
>> cd /data/galaxy-dist/database/job_working_directory/038/38413
>> rm -rf working; mkdir -p working; cd working;
>> /data/galaxy-dist/database/job_working_directory/038/38413/tool_script.sh;
>> return_code=$?; cd
>> '/data/galaxy-dist/database/job_working_directory/038/38413';
>> if [ "$GALAXY_LIB" != "None" ]; then
>>     if [ -n "$PYTHONPATH" ]; then
>>         PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
>>     else
>>         PYTHONPATH="$GALAXY_LIB"
>>     fi
>>     export PYTHONPATH
>> fi
>> if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV"      -a -f
>> "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then
>>     . "$GALAXY_VIRTUAL_ENV/bin/activate"
>> fi
>> GALAXY_PYTHON=`command -v python`
>> export
>> PATH=$PATH:'/data/galaxy-dist/tool_dependency/_conda/envs/__samtools@1.3.1/bin'
>> ; python
>> "/data/galaxy-dist/database/job_working_directory/038/38413/set_metadata_c9AkjG.py"
>> "/data/galaxy-dist/database/job_working_directory/038/38413/registry.xml"
>>
>> "/data/galaxy-dist/database/job_working_directory/038/38413/working/galaxy.json"
>>
>> "/data/galaxy-dist/database/job_working_directory/038/38413/metadata_in_HistoryDatasetAssociation_72822_Eqsgna,/data/galaxy-dist/database/job_working_directory/038/38413/metadata_kwds_HistoryDatasetAssociation_72822_3VQ3be,/data/galaxy-dist/database/job_working_directory/038/38413/metadata_out_HistoryDatasetAssociation_72822_TQg8Pq,/data/galaxy-dist/database/job_working_directory/038/38413/metadata_results_HistoryDatasetAssociation_72822_ctopJa,/data/galaxy-dist/database/files/080/dataset_80995.dat,/data/galaxy-dist/database/job_working_directory/038/38413/metadata_override_HistoryDatasetAssociation_72822_Izp4CZ"
>> 5242880; sh -c "exit $return_code"
>> echo $? >
>> /data/galaxy-dist/database/job_working_directory/038/38413/galaxy_38413.ec
>> date +"%s" >
>> /data/galaxy-dist/database/job_working_directory/038/38413/__instrument_core_epoch_end
>>
>>
>> May be my galaxy.ini in not well configured for conda.
>> For the moment concerning conda in galaxy.ini, I have these lines
>> uncommented :
>>
>> preserve_python_environment = legacy_and_local
>> dependency_resolvers_config_file = config/dependency_resolvers_conf.xml
>>
>>
>>
>> 2017-10-03 9:53 GMT+02:00 Marius van den Beek <[hidden email]>:
>> > Also upon re-reading I see that your dependency is being picked up from
>> > /usr/local/bin,
>> > which indicates that this isn't using conda at all.
>> > A small excerpt from the logs when you try to run the tool may be
>> > helpful
>> > to understand what is going on there.
>> >
>> > Best,
>> > Marius
>> >
>> > On 3 October 2017 at 09:29, Marius van den Beek <[hidden email]>
>> > wrote:
>> >>
>> >> Hi Julie,
>> >>
>> >> any chance you are setting PYTHONPATH before starting galaxy's job
>> >> handlers (a common place would the supervisor config, in case you're
>> >> using
>> >> that)?
>> >> This will interfere with all python modules that are installed via
>> >> conda.
>> >>
>> >> Best,
>> >> Marius
>> >>
>> >> On 3 October 2017 at 09:13, julie dubois <[hidden email]> wrote:
>> >>>
>> >>> Dear Greg,
>> >>> I read your discussion with @bgruening and I think it's not exactly
>> >>> the same. Because in my case, The executable IS present in my
>> >>> galaxy-dist/tool_dependency/_conda/envs/__deeptools@2.5.1/bin .
>> >>> The problem is far away in the execution when the tool (computeMatrix
>> >>> in my example) try to load the python module deeptools.computeMatrix.
>> >>> So is there a solution to discover where is the problem ?
>> >>>
>> >>> Thanks
>> >>>
>> >>> 2017-10-02 15:16 GMT+02:00 Von Kuster, Greg <[hidden email]>:
>> >>> > This looks like the issue I’ve recently seen as well - I just
>> >>> > discussed
>> >>> > this
>> >>> > with @bgruening on gitter - https://gitter.im/galaxy-iuc/iuc.  I’m
>> >>> > using a
>> >>> > work-around of creating the __deeptools conda env manually.  In my
>> >>> > case, I’m
>> >>> > not installing the whole suite, just the bamCoverage tool from the
>> >>> > TS -
>> >>> >
>> >>> >
>> >>> > https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_bam_coverage/5d11599b8a7d.
>> >>> > My work-around is to create the conda env manually:
>> >>> >
>> >>> > $conda create -n __deeptools@2.5.1 deep tools=2.5.1
>> >>> >
>> >>> > This env is created in the conda environment outside of Galaxy, so I
>> >>> > just
>> >>> > copy it to the conda environment I’ve configured for Galaxy.  This
>> >>> > works,
>> >>> > but it seems there is some issue with the installation from the TS,
>> >>> > so
>> >>> > perhaps a more ling term fix is needed.
>> >>> >
>> >>> >
>> >>> > On Oct 2, 2017, at 8:59 AM, julie dubois <[hidden email]> wrote:
>> >>> >
>> >>> > Hi dev team,
>> >>> >
>> >>> > I have a very big problem since I updated to galaxy 17.05 with
>> >>> > deeptools from toolshed.
>> >>> >
>> >>> > Due to a bug in galaxy 17.05 with toolshed installed tools (reported
>> >>> > in this issue https://github.com/galaxyproject/galaxy/issues/4591),
>> >>> > I
>> >>> > re-installed deeptools to try to resolve it.
>> >>> > Not resolved really but it's another problem. I temporarly bypassed
>> >>> > it.
>> >>> >
>> >>> > Here is my problem : I've installed deeptools from toolshed and when
>> >>> > we try to use "compute matrix" for example, we have this error
>> >>> > message
>> >>> > :
>> >>> >
>> >>> > Fatal error: Exit code 1 ()
>> >>> > Traceback (most recent call last):
>> >>> >  File "/usr/local/bin/computeMatrix", line 4, in <module>
>> >>> >    from deeptools.computeMatrix import main
>> >>> > ImportError: No module named deeptools.computeMatrix
>> >>> >
>> >>> > It seems that wrapper are installed but not the tool "deeptools".
>> >>> >
>> >>> > For more information, here it's the way for the installation :
>> >>> > search and install via toolshed
>> >>> > Install "suite_deeptools" (version 2.5.1.1.0 : 3d68b716965a)
>> >>> > Info in Manage tool dependencies : version=2.5.1, resolver=Conda,
>> >>> > green check symbol in the line with a list of all deeptools.
>> >>> >
>> >>> > Galaxy 17.05, commit cfabe37 (21 sept 2017)
>> >>> >
>> >>> > I've tried to uninstall/reinstall dependencies with conda but
>> >>> > without
>> >>> > success.
>> >>> >
>> >>> > Have you any idea to install the deeptools please ?
>> >>> >
>> >>> > Thanks.
>> >>> > Julie
>> >>> > ___________________________________________________________
>> >>> > 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/
>> >>> >
>> >>> >
>> >>> ___________________________________________________________
>> >>> 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/
>> >>
>> >>
>> >
>
>
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