Re: [galaxy-dev] How to get cleanup script to run in cron job ?

[James Mullan]

Hi Geert,
 I only saw your reply just now when I checked the archive. I
can confirm that I arrived at the same solution myself via
http://stackoverflow.com/questions/3287038/cron-and-virtualenv but Thankyou
for posting your reply. stackoverflow is a great resource as well as this
one.
Many Thanks!

Regards
jamesp

Regards
  Paddy
J P Mullan

On 19 November 2014 at 22:14, James Mullan  wrote:

> Hello,
>  I am trying to figure out how to run the cleanup scripts in a
> cron job. The below works on command line:
>
>  python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d
> 30 -1 -i
> pysqlite>=2 egg successfully loaded for sqlite dialect
> ##
>
> # 2014-11-19 22:07:32 - Handling stuff older than 30 days
> # Displaying info only ( --info_only )
>
> Deleted 0 histories
> Elapsed time:  0.0684289932251
> ##
>
> but if I try to do this in a cron job as follows:
>
>
> 55 21 * * * python scripts/cleanup_datasets/cleanup_datasets.py
> config/galaxy.ini -d 30 -1 -i >> /media/Store/galaxy/galaxy-dist/temp 2>&1
>
> python: can't open file 'scripts/cleanup_datasets/cleanup_datasets.py':
> [Errno 2] No such file or directory
>
> or if I try to do this :
>
>
> 00 22 * * * python
> /media/Store/galaxy/galaxy-dist/scripts/cleanup_datasets/cleanup_datasets.py
> config/galaxy.ini -d 30 -1 -i >> /media/Store/galaxy/galaxy-dist/temp 2>&1
>
> Traceback (most recent call last):
>   File
> "/media/Store/galaxy/galaxy-dist/scripts/cleanup_datasets/cleanup_datasets.py",
> line 13, in 
> from galaxy import eggs
> ImportError: No module named galaxy
>
>
> Note that I am directing the output to a file only to try to find out why
> it's not working.
>
>
> Is this a problem with environment?
>
> Any suggestions what to try would be much appreciated.
>
> Regards
>
> ​James​
>
> J P Mullan
>
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[galaxy-dev] samtools: command not found in bowtie2

[Anna Terry]

Hi,
I installed bowtie2 from the toolshed, but get the following error when I
run it:

Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py",
line 129, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line
998, in finish
dataset.datatype.set_meta( dataset, overwrite=False )  # call
datatype.set_meta directly for the initial set_meta call during
dataset creation
  File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line
251, in set_meta
raise Exception, "Error Setting BAM Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found

I'm not sure why this won't work?
samtools is a dependency for the bowtie2 tool and is installed, but cannot
seem to find it.
There must me something slightly wrong on my server as I can't see loads of
errors like this on this mailing list.

I have added the path from the samtools env file to .bash_profile for
galaxy and this allows this tool to run,  but is not the correct solution,
as doesn't work when versions change.

Could you let me know where I'm going wrong
Thanks
Anna
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Re: [galaxy-dev] samtools: command not found in bowtie2

[Eric Kuyt]

Hi Anna,

Setting your own path variables shouldn't be necessary for toolshed tools,
so probably something is wrong with the installation. could you post your

tooldependencies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/INSTALLATION.log

file?

On 26 November 2014 at 13:49, Anna Terry  wrote:

> Hi,
> I installed bowtie2 from the toolshed, but get the following error when I
> run it:
>
>
> Traceback (most recent call last):
>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line
> 129, in queue_job
> job_wrapper.finish( stdout, stderr, exit_code )
>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998,
> in finish
> dataset.datatype.set_meta( dataset, overwrite=False )  # call
> datatype.set_meta directly for the initial set_meta call during dataset
> creation
>   File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line
> 251, in set_meta
> raise Exception, "Error Setting BAM Metadata: %s" % stderr
> Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
>
> I'm not sure why this won't work?
> samtools is a dependency for the bowtie2 tool and is installed, but cannot
> seem to find it.
> There must me something slightly wrong on my server as I can't see loads
> of errors like this on this mailing list.
>
> I have added the path from the samtools env file to .bash_profile for
> galaxy and this allows this tool to run,  but is not the correct solution,
> as doesn't work when versions change.
>
> Could you let me know where I'm going wrong
> Thanks
> Anna
>



-- 
Central Veterinary Institute of Wageningen UR (CVI)
Department of Infection Biology
PO box 65, 8200 AB Lelystad, NL
Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad

Tel:  +31-(0)320-293391
Fax: +31-(0)320-238153
E-mail: eric.ku...@wur.nl
Web: http://www.cvi.wur.nl
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Re: [galaxy-dev] samtools: command not found in bowtie2

[Björn Grüning]

Hi Anna,

you need to install samtools into your system or via the toolshed. If
you install it via the toolshed you need to create a symlink.

Lets assume you have samtools installed in:

~/tool_deps/samtools/0.19/iuc/2828727744/

than you need to create a symlink from
~/tool_deps/samtools/0.19/iuc/2828727744/ to ~/tool_deps/samtools/default

Hope this helps,
Bjoern

Am 26.11.2014 um 13:49 schrieb Anna Terry:
> Hi,
> I installed bowtie2 from the toolshed, but get the following error when I
> run it:
> 
> Traceback (most recent call last):
>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py",
> line 129, in queue_job
> job_wrapper.finish( stdout, stderr, exit_code )
>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line
> 998, in finish
> dataset.datatype.set_meta( dataset, overwrite=False )  # call
> datatype.set_meta directly for the initial set_meta call during
> dataset creation
>   File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line
> 251, in set_meta
> raise Exception, "Error Setting BAM Metadata: %s" % stderr
> Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
> 
> I'm not sure why this won't work?
> samtools is a dependency for the bowtie2 tool and is installed, but cannot
> seem to find it.
> There must me something slightly wrong on my server as I can't see loads of
> errors like this on this mailing list.
> 
> I have added the path from the samtools env file to .bash_profile for
> galaxy and this allows this tool to run,  but is not the correct solution,
> as doesn't work when versions change.
> 
> Could you let me know where I'm going wrong
> Thanks
> Anna
> 
> 
> 
> ___
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> 
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Re: [galaxy-dev] importing a large number of samples via a sample sheet

[Dannon Baker]

Hey Ryan,

Sorry this took a long while for me to get back to, again.  I probably
should have pointed you here to start with, but bioblend (a nice python
layer on top of the raw galaxy API)  has a much friendlier interface and is
what you'd probably want to use for this kind of script.  Here's an example
specifically of uploading from filepaths to a data library:

http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/docs.html#upload-files-to-a-data-library

-Dannon


On Thu, Nov 13, 2014 at 1:51 PM, Ryan G  wrote:

> I guess I am going to need a little help to get started...
>
> I'm trying to use display.py.   I've followed the directions and created
> an api key.  When I run:
>
> ./display.py my_key http://myhost:myport/api/libraries
>
> I get the a 403 forbidden.  however, when I enter the URL in a brower:
>
> http://myhost:myport/api/libraries?key=my_key
>
> I get a JSON response with the libraries I've already added.  Something
> must be wrong at the script level?
>
>
>
> On Thu, Nov 13, 2014 at 12:50 PM, Ryan G 
> wrote:
>
>> Let me see if I can find what I need and if I need any help, I'll let you
>> know.  Thanks!
>>
>> On Thu, Nov 13, 2014 at 12:14 PM, Dannon Baker 
>> wrote:
>>
>>> Hey Ryan,
>>>
>>> Sorry this fell through the cracks.  A script to import large sets of
>>> files to data libraries, for example, would be really easy to implement
>>> using the Galaxy API.  There are several examples in the /scripts/api
>>> folder of your distribution (
>>> https://bitbucket.org/galaxy/galaxy-central/src/7f247bf156dfc7cfa7f764cf9757ae3839f0b72c/scripts/api/?at=default).
>>> I can find an explicit example of this if you're interested.
>>>
>>> -Dannon
>>>
>>> On Thu, Nov 13, 2014 at 9:08 AM, Ryan G 
>>> wrote:
>>>
 Bumping this questionno response in over a week...

 Hi all - I've recently come back to Galaxy to see how its progressed
 over the last few years.  The tools shed is completely new to me and will
 take some exploring on my part.

 My immediate question is if there is a way to import a large number of
 samples associated with a project via a sample sheet (txt) file?  I have a
 text file with 3 columns: sample name, location of fastq files.

 I haven't seen a way to import this and haven't seen anything in the
 docs either.  I suspect the answer is no, but I'm hoping the answer is
 actually yes?

 ___
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>>>
>>>
>>
>
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Re: [galaxy-dev] Egg build failed for bx_python 0.7.2

[Dannon Baker]

Are you sure you need to build your own eggs?  Outside a few
cluster-specific eggs, this is rarely the case (and not for bx-python, to
my knowledge).

The first thing I'd check is whether or not removing the eggs directory (to
force a clean start from whatever egg situation you have now) from Galaxy
and just running 'sh run.sh' will fetch the correct eggs for you
automatically, without requiring local compilation.   This *should*
automatically fetch pre-scrambled eggs from our servers correct for your
architecture.

-Dannon

On Tue, Nov 25, 2014 at 9:48 AM, Rafael Guerrero-Preston 
wrote:

>  I have sensitive clinical data and would like to run Galaxy on a local
> production server. While creating/acquiring the required Python eggs to
> start the server for the first time using the *sh run.sh* command I got
> the following error message.  How should I proceed?
>
>
>  gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -arch ppc -arch i386
> -g -O2 -DNDEBUG -g -O3 -Isrc/kent -Isrc
> -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c
> lib/bx/bitset.c -o build/temp.macosx-10.3-fat-2.7/lib/bx/bitset.o
>
> unable to execute gcc-4.0: No such file or directory
>
> error: command 'gcc-4.0' failed with exit status 1
>
> Traceback (most recent call last):
>
>   File "scripts/scramble.py", line 50, in 
>
> egg.scramble()
>
>   File
> "/Users/rafaelguerrero-preston/galaxy-dist/lib/galaxy/eggs/scramble.py",
> line 57, in scramble
>
> self.run_scramble_script()
>
>   File
> "/Users/rafaelguerrero-preston/galaxy-dist/lib/galaxy/eggs/scramble.py",
> line 206, in run_scramble_script
>
> raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % (
> sys._getframe().f_code.co_name, self.name, self.version ) )
>
> galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build
> failed for bx_python 0.7.2
>
>
> ___
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>
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Re: [galaxy-dev] samtools: command not found in bowtie2

[Anna Terry]

So I actually still have a problem,
(I guess the setting was still there somewhere from the bash_profile)

Anyway, I am also getting the problem with samtools filter sam or bam

Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py",
line 129, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line
998, in finish
dataset.datatype.set_meta( dataset, overwrite=False )  # call
datatype.set_meta directly for the initial set_meta call during
dataset creation
  File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line
251, in set_meta
raise Exception, "Error Setting BAM Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found

I have tried also what you said, linking the samtools binary to
default, but still the same problem.

Any other ideas?



On 26 November 2014 at 14:01, Anna Terry  wrote:

> Great, I've done it and it works.
>
> galaxy-dist/tools/samtools/default
> cd galaxy-dist/tools/samtools/default/
> cp -rs ~/galaxy-dist/tools/samtools/0.1.19/* .
>
> Thanks Bjoern and Eric
>
>
> On 26 November 2014 at 13:54, Eric Kuyt  wrote:
>
>> Bjoerns comment was the right one, samtools isn't automatically installed
>> as a dependency somehow.
>>
>> so the best option is to install samtools
>> https://toolshed.g2.bx.psu.edu/view/devteam/package_samtools_0_1_19
>>
>> and link the installed binary to ~/tool_deps/samtools/0.19/iuc/2828727744/
>> to ~/tool_deps/samtools/default
>>
>> Eric
>>
>>
>> On 26 November 2014 at 14:44, Anna Terry 
>> wrote:
>>
>>> Here is the contents of the log file:
>>>
>>> Successfully downloaded from url:
>>> http://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.1.0-linux-x86_64.tgz
>>>
>>>
>>> On 26 November 2014 at 13:26, Eric Kuyt >> eric.ku...@wur.nl>> wrote:
>>> Hi Anna,
>>>
>>> Setting your own path variables shouldn't be necessary for toolshed
>>> tools, so probably something is wrong with the installation. could you post
>>> your
>>>
>>>
>>> tooldependencies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/INSTALLATION.log
>>>
>>> file?
>>>
>>> On 26 November 2014 at 13:49, Anna Terry >> > wrote:
>>> Hi,
>>> I installed bowtie2 from the toolshed, but get the following error when
>>> I run it:
>>>
>>>
>>> Traceback (most recent call last):
>>>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line
>>> 129, in queue_job
>>> job_wrapper.finish( stdout, stderr, exit_code )
>>>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998,
>>> in finish
>>> dataset.datatype.set_meta( dataset, overwrite=False )  # call
>>> datatype.set_meta directly for the initial set_meta call during dataset
>>> creation
>>>   File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line
>>> 251, in set_meta
>>> raise Exception, "Error Setting BAM Metadata: %s" % stderr
>>> Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not
>>> found
>>>
>>> I'm not sure why this won't work?
>>> samtools is a dependency for the bowtie2 tool and is installed, but
>>> cannot seem to find it.
>>> There must me something slightly wrong on my server as I can't see loads
>>> of errors like this on this mailing list.
>>>
>>> I have added the path from the samtools env file to .bash_profile for
>>> galaxy and this allows this tool to run,  but is not the correct solution,
>>> as doesn't work when versions change.
>>>
>>> Could you let me know where I'm going wrong
>>> Thanks
>>> Anna
>>>
>>>
>>>
>>> --
>>> Central Veterinary Institute of Wageningen UR (CVI)
>>> Department of Infection Biology
>>> PO box 65, 8200 AB Lelystad, NL
>>> Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
>>>
>>> Tel:  +31-(0)320-293391
>>> Fax: +31-(0)320-238153
>>> E-mail: eric.ku...@wur.nl
>>> Web: http://www.cvi.wur.nl
>>>
>>>
>>
>>
>> --
>> Central Veterinary Institute of Wageningen UR (CVI)
>> Department of Infection Biology
>> PO box 65, 8200 AB Lelystad, NL
>> Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
>>
>> Tel:  +31-(0)320-293391
>> Fax: +31-(0)320-238153
>> E-mail: eric.ku...@wur.nl
>> Web: http://www.cvi.wur.nl
>>
>
>
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Re: [galaxy-dev] samtools: command not found in bowtie2

[Anna Terry]

What is really weird is when running the bowtie2 tool, before it quits, I
can see samtools come up in top

On 26 November 2014 at 15:55, Anna Terry  wrote:

> So I actually still have a problem,
> (I guess the setting was still there somewhere from the bash_profile)
>
> Anyway, I am also getting the problem with samtools filter sam or bam
>
> Traceback (most recent call last):
>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, 
> in queue_job
> job_wrapper.finish( stdout, stderr, exit_code )
>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in 
> finish
> dataset.datatype.set_meta( dataset, overwrite=False )  # call 
> datatype.set_meta directly for the initial set_meta call during dataset 
> creation
>   File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, 
> in set_meta
> raise Exception, "Error Setting BAM Metadata: %s" % stderr
> Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
>
> I have tried also what you said, linking the samtools binary to default, but 
> still the same problem.
>
> Any other ideas?
>
>
>
> On 26 November 2014 at 14:01, Anna Terry  wrote:
>
>> Great, I've done it and it works.
>>
>> galaxy-dist/tools/samtools/default
>> cd galaxy-dist/tools/samtools/default/
>> cp -rs ~/galaxy-dist/tools/samtools/0.1.19/* .
>>
>> Thanks Bjoern and Eric
>>
>>
>> On 26 November 2014 at 13:54, Eric Kuyt  wrote:
>>
>>> Bjoerns comment was the right one, samtools isn't automatically
>>> installed as a dependency somehow.
>>>
>>> so the best option is to install samtools
>>> https://toolshed.g2.bx.psu.edu/view/devteam/package_samtools_0_1_19
>>>
>>> and link the installed binary to ~/tool_deps/samtools/0.19/iuc/2828727744/
>>> to ~/tool_deps/samtools/default
>>>
>>> Eric
>>>
>>>
>>> On 26 November 2014 at 14:44, Anna Terry 
>>> wrote:
>>>
 Here is the contents of the log file:

 Successfully downloaded from url:
 http://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.1.0-linux-x86_64.tgz


 On 26 November 2014 at 13:26, Eric Kuyt >>> eric.ku...@wur.nl>> wrote:
 Hi Anna,

 Setting your own path variables shouldn't be necessary for toolshed
 tools, so probably something is wrong with the installation. could you post
 your


 tooldependencies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/INSTALLATION.log

 file?

 On 26 November 2014 at 13:49, Anna Terry >>> > wrote:
 Hi,
 I installed bowtie2 from the toolshed, but get the following error when
 I run it:


 Traceback (most recent call last):
   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py",
 line 129, in queue_job
 job_wrapper.finish( stdout, stderr, exit_code )
   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line
 998, in finish
 dataset.datatype.set_meta( dataset, overwrite=False )  # call
 datatype.set_meta directly for the initial set_meta call during dataset
 creation
   File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line
 251, in set_meta
 raise Exception, "Error Setting BAM Metadata: %s" % stderr
 Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not
 found

 I'm not sure why this won't work?
 samtools is a dependency for the bowtie2 tool and is installed, but
 cannot seem to find it.
 There must me something slightly wrong on my server as I can't see
 loads of errors like this on this mailing list.

 I have added the path from the samtools env file to .bash_profile for
 galaxy and this allows this tool to run,  but is not the correct solution,
 as doesn't work when versions change.

 Could you let me know where I'm going wrong
 Thanks
 Anna



 --
 Central Veterinary Institute of Wageningen UR (CVI)
 Department of Infection Biology
 PO box 65, 8200 AB Lelystad, NL
 Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad

 Tel:  +31-(0)320-293391
 Fax: +31-(0)320-238153
 E-mail: eric.ku...@wur.nl
 Web: http://www.cvi.wur.nl


>>>
>>>
>>> --
>>> Central Veterinary Institute of Wageningen UR (CVI)
>>> Department of Infection Biology
>>> PO box 65, 8200 AB Lelystad, NL
>>> Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
>>>
>>> Tel:  +31-(0)320-293391
>>> Fax: +31-(0)320-238153
>>> E-mail: eric.ku...@wur.nl
>>> Web: http://www.cvi.wur.nl
>>>
>>
>>
>
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Re: [galaxy-dev] samtools: command not found in bowtie2

[Eric Kuyt]

​Could you try going to Admin -> Manage Installed tool shed repositories

uninstall -> reinstall ​package_samtools_0_1_18


On 26 November 2014 at 16:55, Anna Terry  wrote:

> yway, I am also getting the problem with samtools filter sam or bam





-- 
Central Veterinary Institute of Wageningen UR (CVI)
Department of Infection Biology
PO box 65, 8200 AB Lelystad, NL
Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad

Tel:  +31-(0)320-293391
Fax: +31-(0)320-238153
E-mail: eric.ku...@wur.nl
Web: http://www.cvi.wur.nl
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Re: [galaxy-dev] samtools: command not found in bowtie2

[Anna Terry]

I just tried still the same problem.
I ran bowtie2 to test, again I saw samtools come up on top, but same error:

Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py",
line 129, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line
998, in finish
dataset.datatype.set_meta( dataset, overwrite=False )  # call
datatype.set_meta directly for the initial set_meta call during
dataset creation
  File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line
251, in set_meta
raise Exception, "Error Setting BAM Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found



On 26 November 2014 at 16:01, Eric Kuyt  wrote:

> ​Could you try going to Admin -> Manage Installed tool shed repositories
>
> uninstall -> reinstall ​package_samtools_0_1_18
>
>
> On 26 November 2014 at 16:55, Anna Terry  wrote:
>
>> yway, I am also getting the problem with samtools filter sam or bam
>
>
>
>
>
> --
> Central Veterinary Institute of Wageningen UR (CVI)
> Department of Infection Biology
> PO box 65, 8200 AB Lelystad, NL
> Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
>
> Tel:  +31-(0)320-293391
> Fax: +31-(0)320-238153
> E-mail: eric.ku...@wur.nl
> Web: http://www.cvi.wur.nl
>
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Re: [galaxy-dev] samtools: command not found in bowtie2

[bjoern.gruen...@googlemail.com]

The problem is that bowtie and Galaxy (can) use a different samtools
version. Galaxy needs samtools to create metadata for BAM files, so this
process is actually running ofter bowtie has finished.
You need a samtools version globally accessible for Galaxy. Make sure you
have smatools in your $PATH and than restart Galaxy.

Cheers,
Bjoern

2014-11-26 17:14 GMT+01:00 Anna Terry :

> I just tried still the same problem.
> I ran bowtie2 to test, again I saw samtools come up on top, but same error:
>
> Traceback (most recent call last):
>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, 
> in queue_job
> job_wrapper.finish( stdout, stderr, exit_code )
>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in 
> finish
> dataset.datatype.set_meta( dataset, overwrite=False )  # call 
> datatype.set_meta directly for the initial set_meta call during dataset 
> creation
>   File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, 
> in set_meta
> raise Exception, "Error Setting BAM Metadata: %s" % stderr
> Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
>
>
>
> On 26 November 2014 at 16:01, Eric Kuyt  wrote:
>
>> ​Could you try going to Admin -> Manage Installed tool shed repositories
>>
>> uninstall -> reinstall ​package_samtools_0_1_18
>>
>>
>> On 26 November 2014 at 16:55, Anna Terry 
>> wrote:
>>
>>> yway, I am also getting the problem with samtools filter sam or bam
>>
>>
>>
>>
>>
>> --
>> Central Veterinary Institute of Wageningen UR (CVI)
>> Department of Infection Biology
>> PO box 65, 8200 AB Lelystad, NL
>> Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
>>
>> Tel:  +31-(0)320-293391
>> Fax: +31-(0)320-238153
>> E-mail: eric.ku...@wur.nl
>> Web: http://www.cvi.wur.nl
>>
>
>
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
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Re: [galaxy-dev] samtools: command not found in bowtie2

[Anna Terry]

is bash_profile the best place for this, or is somewhere else better?

Cheers
Anna

On 26 November 2014 at 16:29, bjoern.gruen...@googlemail.com <
bjoern.gruen...@gmail.com> wrote:

> The problem is that bowtie and Galaxy (can) use a different samtools
> version. Galaxy needs samtools to create metadata for BAM files, so this
> process is actually running ofter bowtie has finished.
> You need a samtools version globally accessible for Galaxy. Make sure you
> have smatools in your $PATH and than restart Galaxy.
>
> Cheers,
> Bjoern
>
> 2014-11-26 17:14 GMT+01:00 Anna Terry :
>
>> I just tried still the same problem.
>> I ran bowtie2 to test, again I saw samtools come up on top, but same
>> error:
>>
>> Traceback (most recent call last):
>>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 
>> 129, in queue_job
>> job_wrapper.finish( stdout, stderr, exit_code )
>>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in 
>> finish
>> dataset.datatype.set_meta( dataset, overwrite=False )  # call 
>> datatype.set_meta directly for the initial set_meta call during dataset 
>> creation
>>   File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, 
>> in set_meta
>> raise Exception, "Error Setting BAM Metadata: %s" % stderr
>> Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
>>
>>
>>
>> On 26 November 2014 at 16:01, Eric Kuyt  wrote:
>>
>>> ​Could you try going to Admin -> Manage Installed tool shed repositories
>>>
>>> uninstall -> reinstall ​package_samtools_0_1_18
>>>
>>>
>>> On 26 November 2014 at 16:55, Anna Terry 
>>> wrote:
>>>
 yway, I am also getting the problem with samtools filter sam or bam
>>>
>>>
>>>
>>>
>>>
>>> --
>>> Central Veterinary Institute of Wageningen UR (CVI)
>>> Department of Infection Biology
>>> PO box 65, 8200 AB Lelystad, NL
>>> Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
>>>
>>> Tel:  +31-(0)320-293391
>>> Fax: +31-(0)320-238153
>>> E-mail: eric.ku...@wur.nl
>>> Web: http://www.cvi.wur.nl
>>>
>>
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>
>
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Re: [galaxy-dev] samtools: command not found in bowtie2

[bjoern.gruen...@googlemail.com]

I would use .bashrc. You can also try to symlib the default dir to the
actual /bin directory. Maybe this works for you.

2014-11-26 17:36 GMT+01:00 Anna Terry :

> is bash_profile the best place for this, or is somewhere else better?
>
> Cheers
> Anna
>
> On 26 November 2014 at 16:29, bjoern.gruen...@googlemail.com <
> bjoern.gruen...@gmail.com> wrote:
>
>> The problem is that bowtie and Galaxy (can) use a different samtools
>> version. Galaxy needs samtools to create metadata for BAM files, so this
>> process is actually running ofter bowtie has finished.
>> You need a samtools version globally accessible for Galaxy. Make sure you
>> have smatools in your $PATH and than restart Galaxy.
>>
>> Cheers,
>> Bjoern
>>
>> 2014-11-26 17:14 GMT+01:00 Anna Terry :
>>
>>> I just tried still the same problem.
>>> I ran bowtie2 to test, again I saw samtools come up on top, but same
>>> error:
>>>
>>> Traceback (most recent call last):
>>>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 
>>> 129, in queue_job
>>> job_wrapper.finish( stdout, stderr, exit_code )
>>>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in 
>>> finish
>>> dataset.datatype.set_meta( dataset, overwrite=False )  # call 
>>> datatype.set_meta directly for the initial set_meta call during dataset 
>>> creation
>>>   File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, 
>>> in set_meta
>>> raise Exception, "Error Setting BAM Metadata: %s" % stderr
>>> Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
>>>
>>>
>>>
>>> On 26 November 2014 at 16:01, Eric Kuyt  wrote:
>>>
 ​Could you try going to Admin -> Manage Installed tool shed repositories

 uninstall -> reinstall ​package_samtools_0_1_18


 On 26 November 2014 at 16:55, Anna Terry 
 wrote:

> yway, I am also getting the problem with samtools filter sam or bam





 --
 Central Veterinary Institute of Wageningen UR (CVI)
 Department of Infection Biology
 PO box 65, 8200 AB Lelystad, NL
 Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad

 Tel:  +31-(0)320-293391
 Fax: +31-(0)320-238153
 E-mail: eric.ku...@wur.nl
 Web: http://www.cvi.wur.nl

>>>
>>>
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>   https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>   http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
>
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Re: [galaxy-dev] samtools: command not found in bowtie2

[Anna Terry]

great, thanks

On 26 November 2014 at 16:39, bjoern.gruen...@googlemail.com <
bjoern.gruen...@gmail.com> wrote:

> I would use .bashrc. You can also try to symlib the default dir to the
> actual /bin directory. Maybe this works for you.
>
> 2014-11-26 17:36 GMT+01:00 Anna Terry :
>
>> is bash_profile the best place for this, or is somewhere else better?
>>
>> Cheers
>> Anna
>>
>> On 26 November 2014 at 16:29, bjoern.gruen...@googlemail.com <
>> bjoern.gruen...@gmail.com> wrote:
>>
>>> The problem is that bowtie and Galaxy (can) use a different samtools
>>> version. Galaxy needs samtools to create metadata for BAM files, so this
>>> process is actually running ofter bowtie has finished.
>>> You need a samtools version globally accessible for Galaxy. Make sure
>>> you have smatools in your $PATH and than restart Galaxy.
>>>
>>> Cheers,
>>> Bjoern
>>>
>>> 2014-11-26 17:14 GMT+01:00 Anna Terry :
>>>
 I just tried still the same problem.
 I ran bowtie2 to test, again I saw samtools come up on top, but same
 error:

 Traceback (most recent call last):
   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 
 129, in queue_job
 job_wrapper.finish( stdout, stderr, exit_code )
   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, 
 in finish
 dataset.datatype.set_meta( dataset, overwrite=False )  # call 
 datatype.set_meta directly for the initial set_meta call during dataset 
 creation
   File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 
 251, in set_meta
 raise Exception, "Error Setting BAM Metadata: %s" % stderr
 Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found



 On 26 November 2014 at 16:01, Eric Kuyt  wrote:

> ​Could you try going to Admin -> Manage Installed tool shed
> repositories
>
> uninstall -> reinstall ​package_samtools_0_1_18
>
>
> On 26 November 2014 at 16:55, Anna Terry 
> wrote:
>
>> yway, I am also getting the problem with samtools filter sam or bam
>
>
>
>
>
> --
> Central Veterinary Institute of Wageningen UR (CVI)
> Department of Infection Biology
> PO box 65, 8200 AB Lelystad, NL
> Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
>
> Tel:  +31-(0)320-293391
> Fax: +31-(0)320-238153
> E-mail: eric.ku...@wur.nl
> Web: http://www.cvi.wur.nl
>


 ___
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>>>
>>>
>>
>
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[galaxy-dev] galaxy fails to start when setuptools>=6.1

[Evan Bollig PhD]

I tested all versions of setuptools available in PyPI from 0.6c11 up
to 7.0. I found that galaxy fails to fetch eggs with the following
error when setuptools > 6.0.2 (i.e., 6.1 and 7.0).

#
 * Creating directory in /mnt for galaxy data
*
Starting Galaxy Galaxy
Some eggs are out of date, attempting to fetch...
Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Traceback (most recent call last):
  File "./scripts/fetch_eggs.py", line 46, in 
c.resolve() # Only fetch eggs required by the config
  File "/opt/galaxy/web/lib/galaxy/eggs/__init__.py", line 347, in resolve
egg.resolve()
  File "/opt/galaxy/web/lib/galaxy/eggs/__init__.py", line 192, in resolve
if e.args[1].key != e.args[0].key:
IndexError: tuple index out of range
Fetch failed.
#

Cheers,
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu
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Re: [galaxy-dev] galaxy fails to start when setuptools>=6.1

[Peter Cock]

Good sleuthing Evan :)

That explains this strange error I was getting:
http://dev.list.galaxyproject.org/MarkupSafe-egg-missing-e-args-1-key-e-args-0-key-tc4666021.html

(In that case I switched to using a virtualenv)

Peter


On Wed, Nov 26, 2014 at 6:11 PM, Evan Bollig PhD  wrote:
> I tested all versions of setuptools available in PyPI from 0.6c11 up
> to 7.0. I found that galaxy fails to fetch eggs with the following
> error when setuptools > 6.0.2 (i.e., 6.1 and 7.0).
>
> #
>  * Creating directory in /mnt for galaxy data
> *
> Starting Galaxy Galaxy
> Some eggs are out of date, attempting to fetch...
> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
> Traceback (most recent call last):
>   File "./scripts/fetch_eggs.py", line 46, in 
> c.resolve() # Only fetch eggs required by the config
>   File "/opt/galaxy/web/lib/galaxy/eggs/__init__.py", line 347, in resolve
> egg.resolve()
>   File "/opt/galaxy/web/lib/galaxy/eggs/__init__.py", line 192, in resolve
> if e.args[1].key != e.args[0].key:
> IndexError: tuple index out of range
> Fetch failed.
> #
>
> Cheers,
> -Evan Bollig
> Research Associate | Application Developer | User Support Consultant
> Minnesota Supercomputing Institute
> 599 Walter Library
> 612 624 1447
> e...@msi.umn.edu
> boll0...@umn.edu
> ___
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[galaxy-dev] how to use api to log into Galaxy?

[xlwang]

Hi,
I will integrate Galaxy with another system. When I logged into this system, 
and clicked a link jump to Galaxy, I hope this user has already logged into 
Galaxy. How to use api to deliver a session or somthing else to Galaxy? 
Now, I can use api to create a  new user in this system and  also in Galaxy.


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