Hey there, I'm not an advanced python developer and have an issue setting up my own galaxy server. I followed the steps on getgalaxy.org and have added ~./galaxy-pyhon to my path. The server comes up and I can see stuff but when I try to import a BAM file I get the following error in the history: Traceback (most recent call last): File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 382, in __main__() File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 374, in __main__ add_file( dataset, registry, json_file, output_path ) File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 314, in add_file if datatype.dataset_content_needs_grooming( output_path ): File "/Users/amir/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in dataset_content_needs_grooming version = self._get_samtools_version() File "/Users/amir/galaxy-dist/lib/galaxy/datatypes/binary.py", line 63, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py", line 594, in __init__ errread, errwrite) File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py", line 1097, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory I tried it on my RedHat server as well and get the same error: Traceback (most recent call last): File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/upload.py", line 382, in __main__() File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/upload.py", line 374, in __main__ add_file( dataset, registry, json_file, output_path ) File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/upload.py", line 314, in add_file if datatype.dataset_content_needs_grooming( output_path ): File "/home/amir/galaxy-python/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in dataset_content_needs_grooming version = self._get_samtools_version() File "/home/amir/galaxy-python/galaxy-dist/lib/galaxy/datatypes/binary.py", line 63, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/usr/lib64/python2.6/subprocess.py", line 633, in __init__ errread, errwrite) File "/usr/lib64/python2.6/subprocess.py", line 1139, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory It's worth mentioning that I was able to import a FASTA file. I also checked the server logs and I see: galaxy.tools DEBUG 2011-06-24 12:21:34,430 Loaded tool: t_test_two_samples 1.0.0 galaxy.tools DEBUG 2011-06-24 12:21:37,993 Loaded tool: sam_indel_filter 1.0.0 galaxy.tools DEBUG 2011-06-24 12:21:38,015 Loaded tool: indel_sam2interval 1.0.0 galaxy.tools DEBUG 2011-06-24 12:21:38,287 Loaded tool: sam_bw_filter 1.0.0 galaxy.tools DEBUG 2011-06-24 12:21:38,304 Loaded tool: sam2interval 1.0.1 galaxy.tools DEBUG 2011-06-24 12:21:38,319 Loaded tool: sam_to_bam 1.1.2 galaxy.tools DEBUG 2011-06-24 12:21:38,331 Loaded tool: bam_to_sam 1.0.3 galaxy.tools DEBUG 2011-06-24 12:21:38,343 Loaded tool: sam_merge 1.1.1 galaxy.tools DEBUG 2011-06-24 12:21:38,371 Loaded tool: sam_pileup 1.1.1 galaxy.tools DEBUG 2011-06-24 12:21:38,497 Loaded tool: samtools_flagstat 1.0.0 So I'm not sure what the issue is... Many thanks in advance for your help! Amir
Amir, Uploading a BAM file in Galaxy requires the Samtools package. You can download it from http://samtools.sourceforge.net/, but if you want more information about installing it (and other NGS tools) in Galaxy, see our wiki page: https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup . Let us know if you need any further assistance. Thanks, Kelly On Fri Jun 24, at 3:46 PM, Amirhossein Kiani wrote:
Hey there,
I'm not an advanced python developer and have an issue setting up my own galaxy server. I followed the steps on getgalaxy.org and have added ~./galaxy-pyhon to my path.
The server comes up and I can see stuff but when I try to import a BAM file I get the following error in the history:
Traceback (most recent call last): File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 382, in
__main__() File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 374, in __main__ add_file( dataset, registry, json_file, output_path ) File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 314, in add_file if datatype.dataset_content_needs_grooming( output_path ): File "/Users/amir/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in dataset_content_needs_grooming version = self._get_samtools_version() File "/Users/amir/galaxy-dist/lib/galaxy/datatypes/binary.py", line 63, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/subprocess.py", line 594, in __init__ errread, errwrite) File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/subprocess.py", line 1097, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
I tried it on my RedHat server as well and get the same error:
Traceback (most recent call last): File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/ upload.py", line 382, in
__main__() File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/ upload.py", line 374, in __main__ add_file( dataset, registry, json_file, output_path ) File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/ upload.py", line 314, in add_file if datatype.dataset_content_needs_grooming( output_path ): File "/home/amir/galaxy-python/galaxy-dist/lib/galaxy/datatypes/ binary.py", line 79, in dataset_content_needs_grooming version = self._get_samtools_version() File "/home/amir/galaxy-python/galaxy-dist/lib/galaxy/datatypes/ binary.py", line 63, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/usr/lib64/python2.6/subprocess.py", line 633, in __init__ errread, errwrite) File "/usr/lib64/python2.6/subprocess.py", line 1139, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
It's worth mentioning that I was able to import a FASTA file.
I also checked the server logs and I see:
galaxy.tools DEBUG 2011-06-24 12:21:34,430 Loaded tool: t_test_two_samples 1.0.0 galaxy.tools DEBUG 2011-06-24 12:21:37,993 Loaded tool: sam_indel_filter 1.0.0 galaxy.tools DEBUG 2011-06-24 12:21:38,015 Loaded tool: indel_sam2interval 1.0.0 galaxy.tools DEBUG 2011-06-24 12:21:38,287 Loaded tool: sam_bw_filter 1.0.0 galaxy.tools DEBUG 2011-06-24 12:21:38,304 Loaded tool: sam2interval 1.0.1 galaxy.tools DEBUG 2011-06-24 12:21:38,319 Loaded tool: sam_to_bam 1.1.2 galaxy.tools DEBUG 2011-06-24 12:21:38,331 Loaded tool: bam_to_sam 1.0.3 galaxy.tools DEBUG 2011-06-24 12:21:38,343 Loaded tool: sam_merge 1.1.1 galaxy.tools DEBUG 2011-06-24 12:21:38,371 Loaded tool: sam_pileup 1.1.1 galaxy.tools DEBUG 2011-06-24 12:21:38,497 Loaded tool: samtools_flagstat 1.0.0
So I'm not sure what the issue is...
Many thanks in advance for your help! Amir ___________________________________________________________ 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:
Many thanks Kelly for your prompt response! I was looking at the tools folder and thought the dependencies are all included. But I can see how that would not make any sense to do :D Cheers, Amir On Jun 24, 2011, at 1:02 PM, Kelly Vincent wrote:
Amir,
Uploading a BAM file in Galaxy requires the Samtools package. You can download it from http://samtools.sourceforge.net/, but if you want more information about installing it (and other NGS tools) in Galaxy, see our wiki page: https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup.
Let us know if you need any further assistance.
Thanks, Kelly
On Fri Jun 24, at 3:46 PM, Amirhossein Kiani wrote:
Hey there,
I'm not an advanced python developer and have an issue setting up my own galaxy server. I followed the steps on getgalaxy.org and have added ~./galaxy-pyhon to my path.
The server comes up and I can see stuff but when I try to import a BAM file I get the following error in the history:
Traceback (most recent call last): File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 382, in
__main__() File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 374, in __main__ add_file( dataset, registry, json_file, output_path ) File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 314, in add_file if datatype.dataset_content_needs_grooming( output_path ): File "/Users/amir/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in dataset_content_needs_grooming version = self._get_samtools_version() File "/Users/amir/galaxy-dist/lib/galaxy/datatypes/binary.py", line 63, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py", line 594, in __init__ errread, errwrite) File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py", line 1097, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
I tried it on my RedHat server as well and get the same error:
Traceback (most recent call last): File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/upload.py", line 382, in
__main__() File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/upload.py", line 374, in __main__ add_file( dataset, registry, json_file, output_path ) File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/upload.py", line 314, in add_file if datatype.dataset_content_needs_grooming( output_path ): File "/home/amir/galaxy-python/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in dataset_content_needs_grooming version = self._get_samtools_version() File "/home/amir/galaxy-python/galaxy-dist/lib/galaxy/datatypes/binary.py", line 63, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/usr/lib64/python2.6/subprocess.py", line 633, in __init__ errread, errwrite) File "/usr/lib64/python2.6/subprocess.py", line 1139, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
It's worth mentioning that I was able to import a FASTA file.
I also checked the server logs and I see:
galaxy.tools DEBUG 2011-06-24 12:21:34,430 Loaded tool: t_test_two_samples 1.0.0 galaxy.tools DEBUG 2011-06-24 12:21:37,993 Loaded tool: sam_indel_filter 1.0.0 galaxy.tools DEBUG 2011-06-24 12:21:38,015 Loaded tool: indel_sam2interval 1.0.0 galaxy.tools DEBUG 2011-06-24 12:21:38,287 Loaded tool: sam_bw_filter 1.0.0 galaxy.tools DEBUG 2011-06-24 12:21:38,304 Loaded tool: sam2interval 1.0.1 galaxy.tools DEBUG 2011-06-24 12:21:38,319 Loaded tool: sam_to_bam 1.1.2 galaxy.tools DEBUG 2011-06-24 12:21:38,331 Loaded tool: bam_to_sam 1.0.3 galaxy.tools DEBUG 2011-06-24 12:21:38,343 Loaded tool: sam_merge 1.1.1 galaxy.tools DEBUG 2011-06-24 12:21:38,371 Loaded tool: sam_pileup 1.1.1 galaxy.tools DEBUG 2011-06-24 12:21:38,497 Loaded tool: samtools_flagstat 1.0.0
So I'm not sure what the issue is...
Many thanks in advance for your help! Amir ___________________________________________________________ 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:
Those errors suggest that the samtools executable could not be found so you'll need to install it and make sure it's available to executing jobs. Galaxy tools rely on a large number of third party executables being installed - these are maintained by other people - see https://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies On Sat, Jun 25, 2011 at 5:46 AM, Amirhossein Kiani <amirhkiani@gmail.com>wrote:
Hey there,
I'm not an advanced python developer and have an issue setting up my own galaxy server. I followed the steps on getgalaxy.org and have added ~./galaxy-pyhon to my path.
The server comes up and I can see stuff but when I try to import a BAM file I get the following error in the history:
Traceback (most recent call last): File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 382, in
__main__() File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 374, in __main__ add_file( dataset, registry, json_file, output_path ) File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 314, in add_file if datatype.dataset_content_needs_grooming( output_path ): File "/Users/amir/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in dataset_content_needs_grooming version = self._get_samtools_version() File "/Users/amir/galaxy-dist/lib/galaxy/datatypes/binary.py", line 63, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py", line 594, in __init__ errread, errwrite) File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py", line 1097, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
I tried it on my RedHat server as well and get the same error:
Traceback (most recent call last): File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/upload.py", line 382, in
__main__() File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/upload.py", line 374, in __main__ add_file( dataset, registry, json_file, output_path ) File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/upload.py", line 314, in add_file if datatype.dataset_content_needs_grooming( output_path ): File "/home/amir/galaxy-python/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in dataset_content_needs_grooming version = self._get_samtools_version() File "/home/amir/galaxy-python/galaxy-dist/lib/galaxy/datatypes/binary.py", line 63, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/usr/lib64/python2.6/subprocess.py", line 633, in __init__ errread, errwrite) File "/usr/lib64/python2.6/subprocess.py", line 1139, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
It's worth mentioning that I was able to import a FASTA file.
I also checked the server logs and I see:
galaxy.tools DEBUG 2011-06-24 12:21:34,430 Loaded tool: t_test_two_samples 1.0.0 galaxy.tools DEBUG 2011-06-24 12:21:37,993 Loaded tool: sam_indel_filter 1.0.0 galaxy.tools DEBUG 2011-06-24 12:21:38,015 Loaded tool: indel_sam2interval 1.0.0 galaxy.tools DEBUG 2011-06-24 12:21:38,287 Loaded tool: sam_bw_filter 1.0.0 galaxy.tools DEBUG 2011-06-24 12:21:38,304 Loaded tool: sam2interval 1.0.1 galaxy.tools DEBUG 2011-06-24 12:21:38,319 Loaded tool: sam_to_bam 1.1.2 galaxy.tools DEBUG 2011-06-24 12:21:38,331 Loaded tool: bam_to_sam 1.0.3 galaxy.tools DEBUG 2011-06-24 12:21:38,343 Loaded tool: sam_merge 1.1.1 galaxy.tools DEBUG 2011-06-24 12:21:38,371 Loaded tool: sam_pileup 1.1.1 galaxy.tools DEBUG 2011-06-24 12:21:38,497 Loaded tool: samtools_flagstat 1.0.0
So I'm not sure what the issue is...
Many thanks in advance for your help! Amir
___________________________________________________________ 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:
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
participants (3)
-
Amirhossein Kiani -
Kelly Vincent -
Ross