Re: [galaxy-dev] Difficulty uploading BAM files
Hi Peter, Thanks to you and all the other responders who were so helpful! This did solve my problem right away. Best regards, Scott On Fri, Feb 26, 2016 at 3:13 PM, Peter Cock wrote: > Hi Scott, > > Galaxy itself requires samtools (to deal with BAM files), separately > from any Tool Dependency within the tool calling framework. > > Right now there is no mechanism for datatype definitions to declare a > dependency (e.g. on a binary like samtools, or a Python library). > > Probably samtools should be listed as a requirement on the wiki? > https://wiki.galaxyproject.org/Admin/GetGalaxy > > Peter > > On Fri, Feb 26, 2016 at 5:49 PM, Scott Szakonyi > wrote: > > Hi, > > > > I'm having trouble uploading BAM files in our development environment. > Other > > files types are uploading without issue. I'm testing with a small BAM > file I > > downloaded, and I'm able to successfully upload it on our production > server > > and usegalaxy.org. When I try to upload in the development environment, > I > > get the following error: > > > > Traceback (most recent call last): > > File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line > > 431, in > > __main__() > > File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line > > 420, in __main__ > > add_file( dataset, registry, json_file, output_path ) > > File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line > > 347, in add_file > > if link_data_only == 'copy_files' and > > datatype.dataset_content_needs_grooming( output_path ): > > File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", > line > > 218, in dataset_content_needs_grooming > > version = self._get_samtools_version() > > File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", > line > > 179, in _get_samtools_version > > raise Exception(message) > > Exception: Attempting to use functionality requiring samtools, but it > cannot > > be located on Galaxy's PATH. > > > > I've checked my installed tools, and all the same Samtools packages are > > successfully installed on the development environment as in production. I > > don't see any missing dependencies or anything like that. At this point > I'm > > stumped. If anyone can offer some guidance on how to resolve this, I'd be > > most appreciative. > > > > Best regards, > > > > -- > > Scott B. Szakonyi > > Research Programmer > > > > Center for Research Computing > > 107 Information Technology Center > > Notre Dame, IN 46556 > > http://crc.nd.edu > > > > ___ > > 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/ > -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Difficulty uploading BAM files
Hi Scott, Galaxy itself requires samtools (to deal with BAM files), separately from any Tool Dependency within the tool calling framework. Right now there is no mechanism for datatype definitions to declare a dependency (e.g. on a binary like samtools, or a Python library). Probably samtools should be listed as a requirement on the wiki? https://wiki.galaxyproject.org/Admin/GetGalaxy Peter On Fri, Feb 26, 2016 at 5:49 PM, Scott Szakonyi wrote: > Hi, > > I'm having trouble uploading BAM files in our development environment. Other > files types are uploading without issue. I'm testing with a small BAM file I > downloaded, and I'm able to successfully upload it on our production server > and usegalaxy.org. When I try to upload in the development environment, I > get the following error: > > Traceback (most recent call last): > File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line > 431, in > __main__() > File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line > 420, in __main__ > add_file( dataset, registry, json_file, output_path ) > File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line > 347, in add_file > if link_data_only == 'copy_files' and > datatype.dataset_content_needs_grooming( output_path ): > File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", line > 218, in dataset_content_needs_grooming > version = self._get_samtools_version() > File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", line > 179, in _get_samtools_version > raise Exception(message) > Exception: Attempting to use functionality requiring samtools, but it cannot > be located on Galaxy's PATH. > > I've checked my installed tools, and all the same Samtools packages are > successfully installed on the development environment as in production. I > don't see any missing dependencies or anything like that. At this point I'm > stumped. If anyone can offer some guidance on how to resolve this, I'd be > most appreciative. > > Best regards, > > -- > Scott B. Szakonyi > Research Programmer > > Center for Research Computing > 107 Information Technology Center > Notre Dame, IN 46556 > http://crc.nd.edu > > ___ > 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] Difficulty uploading BAM files
It is a shame and a but surprising that unlike most other dependencies samtools can not come from an egg now wheel. Christian From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of Marius van den Beek [m.vandenb...@gmail.com] Sent: Friday, February 26, 2016 6:01 PM To: Scott Szakonyi Cc: Galaxy Dev Mailing List Subject: Re: [galaxy-dev] Difficulty uploading BAM files Hello Scott, you do need a samtools binary on GALAXY's PATH. This is not samtools installed from the toolshed. Best, Marius On 26 February 2016 at 18:49, Scott Szakonyi mailto:scott.b.szakony...@nd.edu>> wrote: Hi, I'm having trouble uploading BAM files in our development environment. Other files types are uploading without issue. I'm testing with a small BAM file I downloaded, and I'm able to successfully upload it on our production server and usegalaxy.org<http://usegalaxy.org>. When I try to upload in the development environment, I get the following error: Traceback (most recent call last): File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 431, in __main__() File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 420, in __main__ add_file( dataset, registry, json_file, output_path ) File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 347, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 218, in dataset_content_needs_grooming version = self._get_samtools_version() File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 179, in _get_samtools_version raise Exception(message) Exception: Attempting to use functionality requiring samtools, but it cannot be located on Galaxy's PATH. I've checked my installed tools, and all the same Samtools packages are successfully installed on the development environment as in production. I don't see any missing dependencies or anything like that. At this point I'm stumped. If anyone can offer some guidance on how to resolve this, I'd be most appreciative. Best regards, -- Scott B. Szakonyi Research Programmer Center for Research Computing 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu<http://crc.nd.edu/> ___ 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] Difficulty uploading BAM files
I too had trouble with BAM files as
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py
Line 201
class Bam( Binary ):
...
def _get_samtools_version( self ):
...
samtools_exec = which('samtools')
Assumes samtools is installed on the server and was not fining one.
I had to install samtools outside of galaxy to get past that.
Christian
University of Manchester
From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of
Scott Szakonyi [scott.b.szakony...@nd.edu]
Sent: Friday, February 26, 2016 5:49 PM
To: Galaxy Dev Mailing List
Subject: [galaxy-dev] Difficulty uploading BAM files
Hi,
I'm having trouble uploading BAM files in our development environment. Other
files types are uploading without issue. I'm testing with a small BAM file I
downloaded, and I'm able to successfully upload it on our production server and
usegalaxy.org<http://usegalaxy.org>. When I try to upload in the development
environment, I get the following error:
Traceback (most recent call last):
File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 431,
in
__main__()
File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 420,
in __main__
add_file( dataset, registry, json_file, output_path )
File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 347,
in add_file
if link_data_only == 'copy_files' and
datatype.dataset_content_needs_grooming( output_path ):
File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", line
218, in dataset_content_needs_grooming
version = self._get_samtools_version()
File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", line
179, in _get_samtools_version
raise Exception(message)
Exception: Attempting to use functionality requiring samtools, but it cannot be
located on Galaxy's PATH.
I've checked my installed tools, and all the same Samtools packages are
successfully installed on the development environment as in production. I don't
see any missing dependencies or anything like that. At this point I'm stumped.
If anyone can offer some guidance on how to resolve this, I'd be most
appreciative.
Best regards,
--
Scott B. Szakonyi
Research Programmer
Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu<http://crc.nd.edu/>
___
Please keep all replies on the list by using "reply all"
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and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] Difficulty uploading BAM files
Hello Scott, you do need a samtools binary on GALAXY's PATH. This is not samtools installed from the toolshed. Best, Marius On 26 February 2016 at 18:49, Scott Szakonyi wrote: > Hi, > > I'm having trouble uploading BAM files in our development environment. > Other files types are uploading without issue. I'm testing with a small BAM > file I downloaded, and I'm able to successfully upload it on our production > server and usegalaxy.org. When I try to upload in the development > environment, I get the following error: > > Traceback (most recent call last): > File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line > 431, in > __main__() > File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line > 420, in __main__ > add_file( dataset, registry, json_file, output_path ) > File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line > 347, in add_file > if link_data_only == 'copy_files' and > datatype.dataset_content_needs_grooming( output_path ): > File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", > line 218, in dataset_content_needs_grooming > version = self._get_samtools_version() > File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", > line 179, in _get_samtools_version > raise Exception(message) > Exception: Attempting to use functionality requiring samtools, but it > cannot be located on Galaxy's PATH. > > I've checked my installed tools, and all the same Samtools packages are > successfully installed on the development environment as in production. I > don't see any missing dependencies or anything like that. At this point I'm > stumped. If anyone can offer some guidance on how to resolve this, I'd be > most appreciative. > > Best regards, > > -- > Scott B. Szakonyi > Research Programmer > > *Center for Research Computing* > 107 Information Technology Center > Notre Dame, IN 46556 > http://crc.nd.edu > > ___ > 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/
[galaxy-dev] Difficulty uploading BAM files
Hi, I'm having trouble uploading BAM files in our development environment. Other files types are uploading without issue. I'm testing with a small BAM file I downloaded, and I'm able to successfully upload it on our production server and usegalaxy.org. When I try to upload in the development environment, I get the following error: Traceback (most recent call last): File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 431, in __main__() File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 420, in __main__ add_file( dataset, registry, json_file, output_path ) File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 347, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 218, in dataset_content_needs_grooming version = self._get_samtools_version() File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 179, in _get_samtools_version raise Exception(message) Exception: Attempting to use functionality requiring samtools, but it cannot be located on Galaxy's PATH. I've checked my installed tools, and all the same Samtools packages are successfully installed on the development environment as in production. I don't see any missing dependencies or anything like that. At this point I'm stumped. If anyone can offer some guidance on how to resolve this, I'd be most appreciative. Best regards, -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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/
