subject:"\[galaxy\-dev\] Troubleshooting BAM file upload issues"

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

2016-03-25 Thread Daniel Blankenberg

Hi Amelia,

I’ve provided a patch below that will disable the html check, so you might be 
able to see the uploaded file content to help with debugging.


Thanks,

Dan


$ git diff
diff --git a/lib/galaxy/datatypes/sniff.py b/lib/galaxy/datatypes/sniff.py
index ff9584d..5b608ee 100644
--- a/lib/galaxy/datatypes/sniff.py
+++ b/lib/galaxy/datatypes/sniff.py
@@ -440,8 +440,6 @@ def handle_uploaded_dataset_file( filename, 
datatypes_registry, ext='auto', is_m
 if check_binary( filename ):
 if not Binary.is_ext_unsniffable(ext) and not 
datatypes_registry.get_datatype_by_extension( ext ).sniff( filename ):
 raise InappropriateDatasetContentError( 'The binary uploaded file 
contains inappropriate content.' )
-elif check_html( filename ):
-raise InappropriateDatasetContentError( 'The uploaded file contains 
inappropriate HTML content.' )
 return ext
 
 AUTO_DETECT_EXTENSIONS = [ 'auto' ]  # should 'data' also cause auto detect?
diff --git a/tools/data_source/upload.py b/tools/data_source/upload.py
index 59fa187..0d659c8 100644
--- a/tools/data_source/upload.py
+++ b/tools/data_source/upload.py
@@ -280,11 +280,6 @@ def add_file( dataset, registry, json_file, output_path ):
 err_msg = "You must manually set the 'File Format' 
to '%s' when uploading %s files." % ( ext.capitalize(), ext )
 file_err( err_msg, dataset, json_file )
 return
-if not data_type:
-# We must have a text file
-if check_html( dataset.path ):
-file_err( 'The uploaded file contains inappropriate HTML 
content', dataset, json_file )
-return
 if data_type != 'binary':
 if link_data_only == 'copy_files':
 if dataset.type in ( 'server_dir', 'path_paste' ) and 
data_type not in [ 'gzip', 'bz2', 'zip' ]:




On Mar 25, 2016, at 2:32 PM, Amelia Ireland <airel...@lbl.gov> wrote:

> Hi Christian,
> 
> Thanks for the tip. I tried this, but to no avail. I think that if the 
> problem was with the file ordering, I wouldn't be able to upload it 
> successfully to other galaxy installations (e.g. the main Galaxy server, 
> Galaxy install on my laptop).
> 
> It seems as though the issue is either the file upload process somehow doing 
> weird things to the file, or something going wrong in launching samtools and 
> running the script to process the uploaded file. 
> 
> Thanks,
> Amelia.
> 
> On 24 March 2016 at 02:03, Christian Brenninkmeijer 
> <christian.brenninkmei...@manchester.ac.uk> wrote:
> 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 <d...@bx.psu.edu> 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 <airel...@lbl.gov> wrote:
> 
>> On 23 March 2016 at 01:00, Björn Grüning <bjoern.gruen...@gmail.com> wrote:
>> Hi Amelia,
>> 
>> can you pleae check if you have samtools installed in your

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

2016-03-25 Thread Amelia Ireland

Hi Christian,

Thanks for the tip. I tried this, but to no avail. I think that if the
problem was with the file ordering, I wouldn't be able to upload it
successfully to other galaxy installations (e.g. the main Galaxy server,
Galaxy install on my laptop).

It seems as though the issue is either the file upload process somehow
doing weird things to the file, or something going wrong in launching
samtools and running the script to process the uploaded file.

Thanks,
Amelia.

On 24 March 2016 at 02:03, Christian Brenninkmeijer <
christian.brenninkmei...@manchester.ac.uk> wrote:

> 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 <d...@bx.psu.edu> 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 <airel...@lbl.gov> wrote:
>>
>> On 23 March 2016 at 01:00, Björn Grüning <bjoern.gruen...@gmail.com>
>> 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:
>>
>> 
>> 
>>   
>>   
>>   
>>   
>>   > versionless="true" />
>> 
>>
>> 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 > object at 0x33c71d0> (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_

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<http://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 
<d...@bx.psu.edu<mailto:d...@bx.psu.edu>> 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 
<airel...@lbl.gov<mailto:airel...@lbl.gov>> wrote:

On 23 March 2016 at 01:00, Björn Grüning 
<bjoern.gruen...@gmail.com<mailto:bjoern.gruen...@gmail.com>> 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<http://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 fil

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

2016-03-23 Thread 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/
> >
> 
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy

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

2016-03-23 Thread 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/
>
___
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/

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

2016-03-23 Thread 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/
>>
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>>http://galaxyproject.org/search/mailinglists/
>>
>>
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Re: [galaxy-dev] Troubleshooting BAM file upload issues

2016-03-23 Thread 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
>
>
>
> ___
> 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

2016-03-23 Thread 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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[galaxy-dev] Troubleshooting BAM file upload issues

2016-03-22 Thread 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/

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

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

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

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

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

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

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

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

[galaxy-dev] Troubleshooting BAM file upload issues

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