samtools installation problems
Hi All, New to galaxy here. I'm having an issue uploading bam files into a local instance of galaxy. I understand that it requires samtools, and I installed the appropriate dependency from the toolshed. However, I get the following error: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 407, in <module> __main__() File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 396, in __main__ add_file( dataset, registry, json_file, output_path ) File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 324, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 147, in dataset_content_needs_grooming version = self._get_samtools_version() File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 129, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/usr/lib/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory Which leads me to believe something is wrong with the install (can't find samtools). The dependency directory is also set. Is there another step I'm missing, or is it better to not install dependencies via the toolshed? Best, Nathan Kipniss
Hi Nathan, is samtools executable in the environment path? Scott
On Dec 31, 2014, at 1:49 PM, Nathan Kipniss <nkipniss@gmail.com> wrote:
Hi All,
New to galaxy here. I'm having an issue uploading bam files into a local instance of galaxy. I understand that it requires samtools, and I installed the appropriate dependency from the toolshed. However, I get the following error:
Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 407, in <module> __main__() File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 396, in __main__ add_file( dataset, registry, json_file, output_path ) File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 324, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 147, in dataset_content_needs_grooming version = self._get_samtools_version() File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 129, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/usr/lib/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
Which leads me to believe something is wrong with the install (can't find samtools). The dependency directory is also set. Is there another step I'm missing, or is it better to not install dependencies via the toolshed? Best, Nathan Kipniss
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So I checked, and it is not. (type not found). I will try some of the methods suggested on the admin/config wiki. ( https://wiki.galaxyproject.org/Admin/Config/ToolDependencies) But something I am confused over is why did the install not go "properly" through the toolshed? Or am I missing something in the directions for install? Best, Nathan On Wed, Dec 31, 2014 at 10:50 AM, Scott Jeschonek <scottj@averesystems.com> wrote:
Hi Nathan,
is samtools executable in the environment path?
Scott
On Dec 31, 2014, at 1:49 PM, Nathan Kipniss <nkipniss@gmail.com> wrote:
Hi All,
New to galaxy here. I'm having an issue uploading bam files into a local instance of galaxy. I understand that it requires samtools, and I installed the appropriate dependency from the toolshed. However, I get the following error:
Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 407, in <module> __main__() File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 396, in __main__ add_file( dataset, registry, json_file, output_path ) File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 324, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 147, in dataset_content_needs_grooming version = self._get_samtools_version() File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 129, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/usr/lib/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
Which leads me to believe something is wrong with the install (can't find samtools). The dependency directory is also set. Is there another step I'm missing, or is it better to not install dependencies via the toolshed?
Best, Nathan Kipniss
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Unfortunately the ToolShed dependency only provides samtools to individual Galaxy tools that declare a dependency on it. However, it allows multiple versions of samtools to be available to different (versions of) Galaxy tools. This does NOT provide a samtools on $PATH for Galaxy itself, and it needs it for uploading and indexing BAM files. Peter On Thursday, January 1, 2015, Nathan Kipniss <nkipniss@gmail.com> wrote:
So I checked, and it is not. (type not found). I will try some of the methods suggested on the admin/config wiki. ( https://wiki.galaxyproject.org/Admin/Config/ToolDependencies)
But something I am confused over is why did the install not go "properly" through the toolshed? Or am I missing something in the directions for install?
Best, Nathan
On Wed, Dec 31, 2014 at 10:50 AM, Scott Jeschonek <scottj@averesystems.com <javascript:_e(%7B%7D,'cvml','scottj@averesystems.com');>> wrote:
Hi Nathan,
is samtools executable in the environment path?
Scott
On Dec 31, 2014, at 1:49 PM, Nathan Kipniss <nkipniss@gmail.com <javascript:_e(%7B%7D,'cvml','nkipniss@gmail.com');>> wrote:
Hi All,
New to galaxy here. I'm having an issue uploading bam files into a local instance of galaxy. I understand that it requires samtools, and I installed the appropriate dependency from the toolshed. However, I get the following error:
Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 407, in <module> __main__() File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 396, in __main__ add_file( dataset, registry, json_file, output_path ) File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 324, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 147, in dataset_content_needs_grooming version = self._get_samtools_version() File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 129, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/usr/lib/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
Which leads me to believe something is wrong with the install (can't find samtools). The dependency directory is also set. Is there another step I'm missing, or is it better to not install dependencies via the toolshed?
Best, Nathan Kipniss
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Hi Nathan, please try the following. ln -s /path/to/your/shed_tools/samtools/0.1.19/devteam/what/ever/ /path/to/your/shed_tools/samttools/default The important part is that it is samtools < 1.0 and that the default link is a link to the folder in which you find the env.sh file. I hope this will tell Galaxy how to find samtools for you. Otherwise simply put the samtools binary into your $PATH. Cheers and happy new year! Bjoern Am 31.12.2014 um 19:49 schrieb Nathan Kipniss:
Hi All,
New to galaxy here. I'm having an issue uploading bam files into a local instance of galaxy. I understand that it requires samtools, and I installed the appropriate dependency from the toolshed. However, I get the following error:
Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 407, in <module> __main__() File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 396, in __main__ add_file( dataset, registry, json_file, output_path ) File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 324, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 147, in dataset_content_needs_grooming version = self._get_samtools_version() File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 129, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/usr/lib/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
Which leads me to believe something is wrong with the install (can't find samtools). The dependency directory is also set. Is there another step I'm missing, or is it better to not install dependencies via the toolshed?
Best, Nathan Kipniss
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Thank you all for the help! Its all running smoothly now. Best, Nathan On Wed, Dec 31, 2014 at 3:50 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Nathan,
please try the following.
ln -s /path/to/your/shed_tools/samtools/0.1.19/devteam/what/ever/ /path/to/your/shed_tools/samttools/default
The important part is that it is samtools < 1.0 and that the default link is a link to the folder in which you find the env.sh file.
I hope this will tell Galaxy how to find samtools for you. Otherwise simply put the samtools binary into your $PATH.
Cheers and happy new year! Bjoern
Am 31.12.2014 um 19:49 schrieb Nathan Kipniss:
Hi All,
New to galaxy here. I'm having an issue uploading bam files into a local instance of galaxy. I understand that it requires samtools, and I installed the appropriate dependency from the toolshed. However, I get the following error:
Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 407, in <module> __main__() File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 396, in __main__ add_file( dataset, registry, json_file, output_path ) File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 324, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 147, in dataset_content_needs_grooming version = self._get_samtools_version() File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 129, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/usr/lib/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
Which leads me to believe something is wrong with the install (can't find samtools). The dependency directory is also set. Is there another step I'm missing, or is it better to not install dependencies via the toolshed?
Best, Nathan Kipniss
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participants (4)
-
Björn Grüning -
Nathan Kipniss -
Peter Cock -
Scott Jeschonek