date:20160324

[galaxy-dev] package_bowtie_2_2_6 error

2016-03-24 Thread changyu_fan


Hello All,

We try to install bowtie2 package in galaxy but failed.

Tool shed: toolshed.g2.bx.psu.edu
Name: package_bowtie_2_2_6
Owner: iuc

Here is the message:

tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 89, in 
extract
   os.chmod( absolute_filepath, unix_permissions )

*"[Errno 2] No such file or directory: 
'./database/tmp/tmp-toolshed-mtdpzqr7H/bowtie2-2.2.6/bowtie2-2.2.6/'"*


Any help will be appreciated.

Thanks

Changyu
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[galaxy-dev] Galaxy CloudMan with Galaxy 16.01

2016-03-24 Thread Enis Afgan

Hello!

*We have released a new version of Galaxy CloudMan on AWS.* CloudMan
 offers an easy way to get a
personal and completely functional instance of Galaxy in the cloud in just
a few minutes, without any manual configuration or imposed quotas. Once
running, you have complete control over Galaxy, including the ability to
install new tools.

Most notable changes include:
 * Galaxy 16.01 release
 * A fine-grained control over auto-scaling options
 * Several fixes to cluster sharing and cloning

See the CHANGELOG
 for a
more complete set of changes.

Give it a whirl at launch.usegalaxy.org or take a look at the Getting
Started 
documentation.
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Re: [galaxy-dev] perl version 5.18.1 repository error

2016-03-24 Thread Philipp Rathert

HHi Marius,

 

Many thanks for this detailed information. I reinstalled the pearl package and 
it has now the 8.25 version as an additional dependency.

 

The tool seems to work as well.

 

Thanks again, I will ignore the 8.22 version.

 

 

Cheers,

 

Philipp

 

From: Marius van den Beek [mailto:m.vandenb...@gmail.com] 
Sent: Donnerstag, 24. März 2016 11:49
To: Rathert, Philipp, Dr. 
Cc: Nicola Soranzo ; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] perl version 5.18.1 repository error

 

Hi Philipp,

 

I believe you have run into a rather complicated problem with perl's 
dependencies.

We (the IUC) have changed from coreutils-8.22 to coreutils-8.25 for exactly the 
reason you are reporting

(`...generated no output for the defined timeout period of 3600.0 seconds`).

So you should update your installation of package_perl_5_18_1.

 

Unfortunately, no stable release of galaxy up till now can handle this change 
of dependencies cleanly.

(16.04 will be the first release that should have no problem with this).

When you are doing an update of package_perl_5_18_1, you should have 
gnu-coreutils-8.25 listed as

one of perl's dependencies, as well as gnu-coreutils-8.22. For the moment the 
best thing you can do is to ignore

the status of gnu-coreutils-8.22. Once you upgrade galaxy to release_16.04 or 
newer, repairing package_perl_5_18_1

will remove gnu-coreutils-8.22 from the list of dependencies of perl.

This should not affect the functionality of perl or meme.

Let us know how it goes

 

Marius

 

On 24 March 2016 at 09:23, Rathert, Philipp, Dr. 
 > wrote:

Dear Nicola,

 

now it looks like package_gnu_coreutils_8_22

is generating an error

 

 


gnu_coreutils 

 

8.22

package

Error

Shutting down process id 23231 because it generated no output for the defined 
timeout period of 3600.0 seconds.



 

 

I didn't find anything an this error on the web and I am not sure how I can fix 
this...

 

cheers,

 

philipp 

-Original message-
From: Nicola Soranzo  >
Sent: Wednesday 23rd March 2016 12:49
To: Rathert, Philipp, Dr.  >; 
galaxy-dev@lists.galaxyproject.org  
Subject: Re: [galaxy-dev] perl version 5.18.1 repository error

Hi Philipp,
can you try to reinstall the tool dependency? Go to the Admin interface, 
"Manage installed tools", click on the "package_perl_xml_parser_expat_2_41", 
then from the "Repository Actions" menu select "Manage tool dependencies", 
select the dependency in error and "Uninstall", then select it again and 
"Install" it.

Cheers,
Nicola

On 23/03/16 08:06, Rathert, Philipp, Dr. wrote:

Dear all,

 

i am trying to install  tool (meme-fimo) which needs 
package_perl_xml_parser_expat_2_41 that has a pearl 5.18.1 dependency.

 

however, although the tool installs just fine it shows that 
package_perl_xml_parser_expat_2_41 has missing dependencies:

 

Tool shed repository:package_perl_xml_parser_expat_2_41 

Tool shed repository changeset revision:1ce3818a8eb9 

Tool dependency status:Error 

Tool dependency installation error:Error installing tool dependency perl 
version 5.18.1: Unable to locate the repository directory for revision 
d905bb415eca of installed repository package_perl_5_18 owned by iuc. 

Tool dependency installation 
directory:././tool_deps/perl/5.18.1/iuc/package_perl_xml_parser_expat_2_41/1ce3818a8eb9

 

Is this an error of my local instance or is the revision missing on the 
toolshed?

 

Thank you very much for your help.

 

Cheers,

 

philipp 

 

 

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Re: [galaxy-dev] perl version 5.18.1 repository error

2016-03-24 Thread Marius van den Beek

Hi Philipp,

I believe you have run into a rather complicated problem with perl's
dependencies.
We (the IUC) have changed from coreutils-8.22 to coreutils-8.25 for exactly
the reason you are reporting
(`...generated no output for the defined timeout period of 3600.0 seconds`).
So you should update your installation of package_perl_5_18_1.

Unfortunately, no stable release of galaxy up till now can handle this
change of dependencies cleanly.
(16.04 will be the first release that should have no problem with this).
When you are doing an update of package_perl_5_18_1, you should have
gnu-coreutils-8.25 listed as
one of perl's dependencies, as well as gnu-coreutils-8.22. For the moment
the best thing you can do is to ignore
the status of gnu-coreutils-8.22. Once you upgrade galaxy to release_16.04
or newer, repairing package_perl_5_18_1
will remove gnu-coreutils-8.22 from the list of dependencies of perl.
This should not affect the functionality of perl or meme.
Let us know how it goes

Marius

On 24 March 2016 at 09:23, Rathert, Philipp, Dr. <
philipp.rath...@ibc.uni-stuttgart.de> wrote:

> Dear Nicola,
>
>
> now it looks like package_gnu_coreutils_8_22
>
> is generating an error
>
>
>
> gnu_coreutils
> 
> 8.22 package Error
> Shutting down process id 23231 because it generated no output for the defined 
> timeout period of 3600.0 seconds.
>
> 
>
>
>
> I didn't find anything an this error on the web and I am not sure how I
> can fix this...
>
>
> cheers,
>
>
> philipp
>
> -Original message-
> *From:* Nicola Soranzo 
> *Sent:* Wednesday 23rd March 2016 12:49
> *To:* Rathert, Philipp, Dr. ;
> galaxy-dev@lists.galaxyproject.org
> *Subject:* Re: [galaxy-dev] perl version 5.18.1 repository error
>
> Hi Philipp,
> can you try to reinstall the tool dependency? Go to the Admin interface,
> "Manage installed tools", click on the
> "package_perl_xml_parser_expat_2_41", then from the "Repository Actions"
> menu select "Manage tool dependencies", select the dependency in error and
> "Uninstall", then select it again and "Install" it.
>
> Cheers,
> Nicola
>
> On 23/03/16 08:06, Rathert, Philipp, Dr. wrote:
>
> Dear all,
>
>
> i am trying to install  tool (meme-fimo) which needs 
> package_perl_xml_parser_expat_2_41
> that has a pearl 5.18.1 dependency.
>
>
> however, although the tool installs just fine it shows that 
> package_perl_xml_parser_expat_2_41
> has missing dependencies:
>
>
> Tool shed repository:package_perl_xml_parser_expat_2_41
> Tool shed repository changeset revision:1ce3818a8eb9
> Tool dependency status:Error
> Tool dependency installation error:Error installing tool dependency perl
> version 5.18.1: Unable to locate the repository directory for revision
> d905bb415eca of installed repository package_perl_5_18 owned by iuc.
> Tool dependency installation directory:
> ././tool_deps/perl/5.18.1/iuc/package_perl_xml_parser_expat_2_41/1ce3818a8eb9
>
> Is this an error of my local instance or is the revision missing on the
> toolshed?
>
> Thank you very much for your help.
>
> Cheers,
>
> philipp
>
>
>
>
> ___
> 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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>
>
>
> ___
> 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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>
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Re: [galaxy-dev] Python 2.7 vs 2.6 for galaxy after 16.01

2016-03-24 Thread Sebastian Schaaf

For us, it was more the fact that we are locked down to a certain OS
version due to our local IT policy and the software repositories don't
provide a newer Python than v2.6.8. It was not the first occasion in terms
of desperately outdated software (recently it's gcc itself), so we are
used to compile from source. Using pre-compiled packages from OpenSUSE
repos is not guaranteed to work properly. For us, it is just another
(larger) paragraph for our setup environment written in Ansible. Overall,
it is quite generic and nearly everything needed by Galaxy is installed in
home scheme.
On top, although we are in a quite tight internal network, we realized
that our OpenSSL is of 'pre-heartbleed' times, so it was a good deal to
re-integrate that. Python, wget and others take advantage from this update
if properly linked. Certificate exchange and SSL version usage have moved
on in the last years, and from time to time we got errors/warnings when
accessing external servers.

> On Wed, Mar 23, 2016 at 10:54 PM, D K  wrote:
>> Great! thanks for the suggestions. I just tried using centos software
>> collections and that seems to work. I'll do some more testing but
>> hopefully
>> it's as simple as that! Is there any reason that most of you who
>> responded
>> have decided to compile your own pythons?
>>
>> D
>
> It sounds like both options are effective.
>
> In my case it was perhaps a choice out of ignorance about just how the
> CentOS software collections works - and fear about the CentOS 6 to 7
> migration.
>
> In our case both the Galaxy server and the cluster is still on CentOS 6,
> so we need to use a custom Python 2.7 on both the Galaxy server and
> also on the cluster nodes - ideally the exact same version so that all
> the wheel dependencies match up for running the set metadata scripts.
>
> I'm hoping that using a custom Python 2.7 installation (from source)
> ought to work in our favour if we have to deal with a mixture of CentOS
> 6 and 7 (although ideally we'd update the cluster and Galaxy server
> together).
>
> Regards,
>
> Peter
>

-- 
Sebastian Schaaf, M.Sc. Bioinformatics
Faculty Coordinator NGS Infrastructure
Chair of Biometry and Bioinformatics
Department of Medical Informatics,
 Biometry and Epidemiology (IBE)
University of Munich
DKTK Munich
Marchioninistr. 15, K U1 808
D-81377 Munich (Germany)
Tel: +49 89 4400 77499

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Re: [galaxy-dev] Troubleshooting BAM file upload issues

2016-03-24 Thread Christian Brenninkmeijer

Try using samtools to sort the BAM before uploading.

samtools sort original.bam  sorted.bam

This will help with two things.

1. Check the original file is not corrupt

2. Put the BAM in the only order galaxy will accept.

Christian
University of Manchester

From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Amelia Ireland [airel...@lbl.gov]
Sent: Wednesday, March 23, 2016 8:24 PM
To: Daniel Blankenberg
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Troubleshooting BAM file upload issues

I'm using the standard 'Upload file' tool, and choosing some local files. I can 
successfully upload these files to the galaxy installation on my laptop and to 
the usegalaxy.org server, but uploading them to the 
galaxy installation on the server results in their appearing to be empty and 
the error message about uploaded file containing inappropriate content.

I'm not sure where to proceed from here. Some things I'd like to explore, but 
am not sure how to do so in Galaxy world, are:

- check that the file has uploaded properly
- manually run the tool script on the input file to ensure there's not some 
error that I'm missing

On 23 March 2016 at 12:53, Daniel Blankenberg 
> wrote:
Hi Amelia,

How are you uploading the files?

If you are using a copy and pasted URL, can you make sure that the example file 
exists and is accessible to the machine where the Galaxy job is running.

A 404 error, for example, can often masquerade as a “The uploaded file contains 
inappropriate HTML content” error (although this shouldn’t be the outcome of 
this tool, it should be a red dataset stating a 404 error, in this case).

Thanks for using Galaxy,

Dan

On Mar 23, 2016, at 3:30 PM, Amelia Ireland 
> wrote:

On 23 March 2016 at 01:00, Björn Grüning 
> wrote:
Hi Amelia,

can you pleae check if you have samtools installed in your PATH?

I've got it in my tool dependencies dir and it's also available as an 
Environment module.

The tools dependencies file looks like this:

Debug messages when the tool runs:

galaxy.tools.deps DEBUG 2016-03-23 12:23:05,556 Building dependency shell 
command for dependency 'samtools'
galaxy.tools.deps DEBUG 2016-03-23 12:23:05,556 Find dependency samtools 
version None
galaxy.tools.deps DEBUG 2016-03-23 12:23:05,556 Resolver tool_shed_packages 
returned  
(isnull? True)
galaxy.tools.deps DEBUG 2016-03-23 12:23:05,556 Resolver galaxy_packages 
returned  
(isnull? True)
galaxy.tools.deps DEBUG 2016-03-23 12:23:05,556 Resolver galaxy_packages 
returned  
(isnull? True)
galaxy.tools.deps DEBUG 2016-03-23 12:23:05,556 Resolver modules returned 

(isnull? False)
galaxy.jobs.runners DEBUG 2016-03-23 12:23:05,567 (217) command is: 
/global/homes/a/aireland/galaxy/database/job_working_directory/000/217/tool_script.sh;
 return_code=$?; 
MODULEPATH=/usr/share/Modules:/usr/share/Modules/modulefiles:/etc/modulefiles:/usr/common/usg/Modules/modulefiles:/usr/syscom/nsg/modulefiles:/usr/common/jgi/Modules/modulefiles;
 export MODULEPATH; eval `/usr/bin/modulecmd sh load samtools`; python 
"/global/homes/a/aireland/galaxy/database/job_working_directory/000/217/set_metadata_NFVQiC.py"
 "/global/homes/a/aireland/galaxy/database/tmp/tmp5vpBro" 
"/global/homes/a/aireland/galaxy/database/job_working_directory/000/217/galaxy.json"

"/global/homes/a/aireland/galaxy/database/job_working_directory/000/217/metadata_in_HistoryDatasetAssociation_349_ZqiKgT,/global/homes/a/aireland/galaxy/database/job_working_directory/000/217/metadata_kwds_HistoryDatasetAssociation_349_CH5HZd,/global/homes/a/aireland/galaxy/database/job_working_directory/000/217/metadata_out_HistoryDatasetAssociation_349_Hb4hhP,/global/homes/a/aireland/galaxy/database/job_working_directory/000/217/metadata_results_HistoryDatasetAssociation_349_2e3dj6,/global/homes/a/aireland/galaxy/database/files/000/dataset_320.dat,/global/homes/a/aireland/galaxy/database/job_working_directory/000/217/metadata_override_HistoryDatasetAssociation_349_pEc2Gh"
 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.local DEBUG 2016-03-23 12:23:05,583 (217) executing job 
script: 
/global/homes/a/aireland/galaxy/database/job_working_directory/000/217/galaxy_217.sh
galaxy.jobs DEBUG 2016-03-23 12:23:05,599 (217) Persisting 
job destination (destination id: local:///)
galaxy.jobs.runners.local DEBUG 2016-03-23 12:23:05,799 execution finished: 
/global/homes/a/aireland/galaxy/database/job_working_directory/000/216/galaxy_216.sh

Am 22.03.2016 um 19:28 schrieb Amelia Ireland:
> I'm setting up a Galaxy instance on a new server and am having some
> issues with BAM file uploads. I'm using the BAM files supplied with
> JBrowse for testing purposes. I have Galaxy installed on my laptop and
> file uploads are

Re: [galaxy-dev] perl version 5.18.1 repository error

2016-03-24 Thread Rathert , Philipp , Dr .

Dear Nicola,



now it looks like package_gnu_coreutils_8_22

is generating an error





gnu_coreutils 

8.22package Error   Shutting down process id 23231 because it generated 
no output for the defined timeout period of 3600.0 seconds.







I didn't find anything an this error on the web and I am not sure how I can fix 
this...




cheers,



philipp 

-Original message-
From: Nicola Soranzo 
Sent: Wednesday 23rd March 2016 12:49
To: Rathert, Philipp, Dr. ; 
galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] perl version 5.18.1 repository error

 Hi Philipp,
 can you try to reinstall the tool dependency? Go to the Admin interface, 
"Manage installed tools", click on the "package_perl_xml_parser_expat_2_41", 
then from the "Repository Actions" menu select "Manage tool dependencies", 
select the dependency in error and "Uninstall", then select it again and 
"Install" it.

 Cheers,
 Nicola

On 23/03/16 08:06, Rathert, Philipp, Dr. wrote:
Dear all,


 

i am trying to install  tool (meme-fimo) which needs 
package_perl_xml_parser_expat_2_41 that has a pearl 5.18.1 dependency.


 

however, although the tool installs just fine it shows that 
package_perl_xml_parser_expat_2_41 has missing dependencies:


 

Tool shed repository:package_perl_xml_parser_expat_2_41 
Tool shed repository changeset revision:1ce3818a8eb9 
Tool dependency status:Error 
Tool dependency installation error:Error installing tool dependency perl 
version 5.18.1: Unable to locate the repository directory for revision 
d905bb415eca of installed repository package_perl_5_18 owned by iuc. 
Tool dependency installation 
directory:././tool_deps/perl/5.18.1/iuc/package_perl_xml_parser_expat_2_41/1ce3818a8eb9

Is this an error of my local instance or is the revision missing on the 
toolshed?

Thank you very much for your help.

Cheers,

philipp 


 




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[galaxy-dev] package_bowtie_2_2_6 error

[galaxy-dev] Galaxy CloudMan with Galaxy 16.01

Re: [galaxy-dev] perl version 5.18.1 repository error

Re: [galaxy-dev] perl version 5.18.1 repository error

Re: [galaxy-dev] Python 2.7 vs 2.6 for galaxy after 16.01

Re: [galaxy-dev] Troubleshooting BAM file upload issues

Re: [galaxy-dev] perl version 5.18.1 repository error

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