Re: [galaxy-dev] Data set too large

[Jennifer Hillman-Jackson]

Hello,

FTP is needed for files over 2 GB by default. Try FTP upload. Please
contact your campus administrator if FTP is not enabled. Your admin is the
best resource for alternatives if FTP is not active and will not be (admin
loads data into libraries, and the like).

https://wiki.galaxyproject.org/Support#Loading_data

Please note that the target FTP server is usually the same as the
instance's base URL and the credentials (email/pass) are the same as for
your Galaxy account on that instance. This information is unique for every
Galaxy instance. Try using Filezilla if you are not comfortable with FTP on
the command line.

Take care,

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Wed, Mar 23, 2016 at 4:28 PM, Tiara Smith 
wrote:

> Hell I am accessing galaxy from a main computer on my university campus. I
> am having difficulty uploading my exome files and keep getting the
> following error prompt:
>
> ndex30_CACCGG_L001-L002_R1_001.bam
> *2.8* GB
> Auto-detect
>
> - Additional Species Are Below -
> *Failed: *File exceeds 2GB. Please use a FTP client.
>
>
>
> Is there a way to increase my file upload limit? my data sets range from
> 1.9GB ro 3.9GB.
>
>
> thank you for your help.
>
> Tiara Smith
>
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[galaxy-dev] Data set too large

[Tiara Smith]

Hell I am accessing galaxy from a main computer on my university campus. I
am having difficulty uploading my exome files and keep getting the
following error prompt:

ndex30_CACCGG_L001-L002_R1_001.bam
*2.8* GB
Auto-detect

- Additional Species Are Below -
*Failed: *File exceeds 2GB. Please use a FTP client.



Is there a way to increase my file upload limit? my data sets range from
1.9GB ro 3.9GB.


thank you for your help.

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

[Peter Cock]

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

[D K]

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

On Tue, Mar 22, 2016 at 2:26 AM, Sebastian Schaaf <
sch...@ibe.med.uni-muenchen.de> wrote:

> Same here for v2.7.11 on SLES 11. If you want to integrate as many modules
> as possible at compilation time (we had to skip four unimportant ones in
> the end) it may be painful with an older OS, but I assume CentOS is a bit
> less recalcitrant than SLES.
> We installed everything in home scheme, which requires proper setup of
> environment variables like $PATH, $LD_LIBRARY_PATH, $PYTHONPATH, etc...
> For us the trigger for switching the Python version was an issue with an
> outdated OpenSSL (just days before the Galaxy announcement regarding the
> coming deprecation of 2.6), so we included the reworked/conmpiled OpenSSL
> libraries first. I would recommend the same for you, if your OpenSSL
> package is  yet to our own dev list toppic. Be prepared for recursive dependency
> issues, if your repository software packages are old.
>
>
>
> > We Iocally compile 2.7.8 and keep it in a distinct location that our
> paths
> > references.
> >
> > This is very easy and has worked well for us.
> >
> > Please excuse any typos -- Sent from my iPhone
> >
> >> On Mar 21, 2016, at 5:32 PM, Peter Cock 
> >> wrote:
> >>
> >> Hi D. K.,
> >>
> >> We're currently trying a locally compiled Python 2.7 (from source)
> >> under the shared Galaxy mount for use with a CentOS 6 cluster
> >> and Galaxy server.
> >>
> >> This seems to be working once we got the $PATH working for
> >> cluster jobs (initially they would try to set the Galaxy metadata
> >> using the system Python 2.6, which would fail).
> >>
> >> I don't know if this is any easier than using the CenOS Software
> >> Collections as suggested by Nicola, especially when it comes to
> >> updating the OS.
> >>
> >> Peter
> >>
> >>> On Mon, Mar 21, 2016 at 5:59 PM, Nicola Soranzo 
> >>> wrote:
> >>> Hi Daniel,
> >>> I've been using python27 from CentOS Software Collections for quite
> >>> some
> >>> time. It's a bit annoying because you have to remember to load it, but
> >>> it is
> >>> surely doable.
> >>>
> >>> Cheers,
> >>> Nicola
> >>>
> >>>
> >>> On 21/03/16 17:46, D K wrote:
> >>>
> >>> Hi Galaxy Devs,
> >>>
> >>> This may be premature but I read that for Galaxy after 16.01 that the
> >>> plan
> >>> is for python 2.6 to no longer be supported. I'm currently running
> >>> CentOS
> >>> 6.6 which uses python 2.6. In order to be able to use newer versions of
> >>> Galaxy is my only option to upgrade to a newer version of CentOS? Is it
> >>> possible to use Conda, RedHat Software Collections or some other
> >>> similar
> >>> method instead of doing this upgrade?
> >>>
> >>> Thanks!
> >>>
> >>>
> >>> ___
> >>> 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/
> >>>
> >>>
> >>>
> >>> ___
> >>> 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/
> >> ___
> >> 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/
> > ___
> > 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:
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>
>
> --
> 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
>
>

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

[Daniel Blankenberg]

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 working fine, so it's evidently an issue with the
> > server and/or OS configuration.
> >
> > Attempting to upload a BAM file returns the message
> >
> > "The uploaded binary file contains inappropriate content"
> >
> > and the upload is empty.
> >
> > The server is running Scientific Linux and uses the Environment Modules
> > system for dependency management. I can successfully upload bed and
> > bigwig files, which suggests that samtools is being loaded and
> > functioning correctly.
> >
> > If someone can suggest some troubleshooting steps, I would be most grateful.
> >
> > Thanks!
> > Amelia
> >
> > Integrated Microbial Genomics (IMG)
> > JGI / LBL
> >
> >
> >
> > ___
> > 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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> and other Galaxy 

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

[Amelia Ireland]

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 working fine, so it's evidently an issue with the
> server and/or OS configuration.
>
> Attempting to upload a BAM file returns the message
>
> "The uploaded binary file contains inappropriate content"
>
> and the upload is empty.
>
> The server is running Scientific Linux and uses the Environment Modules
> system for dependency management. I can successfully upload bed and
> bigwig files, which suggests that samtools is being loaded and
> functioning correctly.
>
> If someone can suggest some troubleshooting steps, I would be most
grateful.
>
> Thanks!
> Amelia
>
> Integrated Microbial Genomics (IMG)
> JGI / LBL
>
>
>
> ___
> 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] Troubleshooting BAM file upload issues

[Amelia Ireland]

Both, unfortunately.
On 23 Mar 2016 00:41, "Hans-Rudolf Hotz"  wrote:

> Hi Amelia
>
> Does this happen with "Auto-detect" or do you pre-set the data type to
> 'bam' ?
>
>
> Regards, Hans-Rudolf
>
>
> On 03/22/2016 07:28 PM, Amelia Ireland wrote:
>
>> 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 working fine, so it's evidently an issue with the
>> server and/or OS configuration.
>>
>> Attempting to upload a BAM file returns the message
>>
>> "The uploaded binary file contains inappropriate content"
>>
>> and the upload is empty.
>>
>> The server is running Scientific Linux and uses the Environment Modules
>> system for dependency management. I can successfully upload bed and
>> bigwig files, which suggests that samtools is being loaded and
>> functioning correctly.
>>
>> If someone can suggest some troubleshooting steps, I would be most
>> grateful.
>>
>> Thanks!
>> Amelia
>>
>> Integrated Microbial Genomics (IMG)
>> JGI / LBL
>>
>>
>>
>> ___
>> 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] automatic adding of a tab in a fastq header

[Fabien Mareuil]

Thank :)!

Fabien

Le 23/03/2016 00:01, Martin Čech a écrit :

Thank you for all the help Peter!

Also this is already backported and fixed in 16.01

Sorry for causing this bug in the first place.
M.

On Tue, Mar 22, 2016, 18:29 Peter Cock > wrote:


Well done for solving this Fabien, with only a small hint from me.
I'm glad to see your suggested fix has already been applied to
the Galaxy repository so should be in the next stable release.

Thank you!

Peter

(Also thank you Martin, Nicola, Dan, etc)


On Tue, Mar 22, 2016 at 8:43 PM, Martin Čech > wrote:
> Thank you very much for solving this Fabien, The PR with your
fix has been
> created here: https://github.com/galaxyproject/galaxy/pull/1985
>
> Martin
>
>
> On Mon, Mar 21, 2016 at 5:43 PM fmareuil > wrote:
>>
>> Hi Peter,
>>
>> I worked on it today and I found  the reason of this bug. In
the upload.py
>> tool, the existence of dataset.space_to_tab is tested. In the
old version of
>> the data library, when the option was unchecked, the value
space_to_tab was
>> None and the test worked. But in the new version the value of
space_to_tab
>> is "False", it's a string and the test "if
dataset.space_to_tab" returns
>> True.
>> It is possible to fix it with a little correction of the
>> "/lib/galaxy/webapps/galaxy/api/lda_datasets.py".
>> I join a patch with this email.
>> I can propose a pull request if you want.
>>
>> Best,
>>
>> Fabien
>>



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

[Philipp Rathert]

Hi Nicola,

 

Now I get this:


 

 perl

5.18.1

package

Error

  File "lib/tool_shed/galaxy_install/install_manager.py", line 123, in 
install_and_build_package_via_fabric
tool_dependency = self.install_and_build_package( install_environment, 
tool_dependency, actions_dict )
  File "lib/tool_shed/galaxy_install/install_manager.py", line 108, in 
install_and_build_package
initial_download=False )
  File 
"lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 
31, in execute_step
initial_download=initial_download )
  File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", 
line 1881, in execute_step
job_name=package_name )
  File 
"lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py", 
line 118, in handle_command
self.log_results( cmd, output, os.path.join( self.install_dir, 
basic_util.INSTALLATION_LOG ) )
  File 
"lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py", 
line 250, in log_results
logfile = open( file_path, 'wb' )

[Errno 2] No such file or directory: 
u'/galaxy-central/tool_deps/perl/5.18.1/iuc/package_perl_5_18/d905bb415eca/INSTALLATION.log'

 

 

 

From: Nicola Soranzo [mailto:nicola.sora...@gmail.com] On Behalf Of Nicola 
Soranzo
Sent: Mittwoch, 23. März 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

[Nicola Soranzo]

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:

perl version 5.18.1 repository error

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] Troubleshooting BAM file upload issues

[Christian Brenninkmeijer]

The bam support is regrettably different to most of Galaxy.

For some reason it can not make use of Wheels installed by Galaxy but has to 
use native samtools.
Giving very confusing error messages such as file not found if samtools is not 
there.

Also your bam files MUST be sorted by coordinates as BAM sorted by name is not 
a format supported by Galaxy.
For those few tools that expect Bam sorted by name you have to sort inside that 
tool.

Which breaks:
https://toolshed.g2.bx.psu.edu/view/iuc/samtools_sort/38ea74bd4054
As it returns a bam file no longer(or never) supported by Galaxy

I have wasted a number of days on these confusing behaviours.

Christian
University of Manchester


From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Wednesday, March 23, 2016 8:00 AM
To: Amelia Ireland; galaxy-dev@u coordinateslists.galaxyproject.org
Subject: Re: [galaxy-dev] Troubleshooting BAM file upload issues

Hi Amelia,

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

Ciao,
Bjoern

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 working fine, so it's evidently an issue with the
> server and/or OS configuration.
>
> Attempting to upload a BAM file returns the message
>
> "The uploaded binary file contains inappropriate content"
>
> and the upload is empty.
>
> The server is running Scientific Linux and uses the Environment Modules
> system for dependency management. I can successfully upload bed and
> bigwig files, which suggests that samtools is being loaded and
> functioning correctly.
>
> If someone can suggest some troubleshooting steps, I would be most grateful.
>
> Thanks!
> Amelia
>
> Integrated Microbial Genomics (IMG)
> JGI / LBL
>
>
>
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[galaxy-dev] perl version 5.18.1 repository error

[Rathert , Philipp , Dr .]

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] Troubleshooting BAM file upload issues

[Björn Grüning]

Hi Amelia,

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

Ciao,
Bjoern

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 working fine, so it's evidently an issue with the
> server and/or OS configuration.
> 
> Attempting to upload a BAM file returns the message
> 
> "The uploaded binary file contains inappropriate content"
> 
> and the upload is empty.
> 
> The server is running Scientific Linux and uses the Environment Modules
> system for dependency management. I can successfully upload bed and
> bigwig files, which suggests that samtools is being loaded and
> functioning correctly.
> 
> If someone can suggest some troubleshooting steps, I would be most grateful.
> 
> Thanks!
> Amelia
> 
> Integrated Microbial Genomics (IMG)
> JGI / LBL
> 
> 
> 
> ___
> 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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