Hi Deepak, this is still strange. But as a general remark, don't try to install package_samtools_1_2 or package_* these are deprecated in favor of Conda packages.
Glad it is working now for you! Ciao, Bjoern On 15.08.2017 16:31, Deepak Tanwar wrote: > Hi Björn, > > I tried again from scratch. > > 1. I have installed galaxy-stable image via Kitematic. > 2. I install samtools: *package_samtools_1_2 (2015-07-17) iuc* > 3. I have uploaded the bam file. Error: > > Traceback (most recent call last): File > "/galaxy-central/tools/data_source/upload.py", line 425, in <module> > __main__() File "/galaxy-central/tools/data_source/upload.py", line 413, > in __main__ add_file( dataset, registry, json_file, output_path ) File > "/galaxy-central/tools/data_source/upload.py", line 340, in add_file if > link_data_only == 'copy_files' and > datatype.dataset_content_needs_grooming( output_path ): File > "/galaxy-central/lib/galaxy/datatypes/binary.py", line 295, in > dataset_content_needs_grooming version = self._get_samtools_version() > File "/galaxy-central/lib/galaxy/datatypes/binary.py", line 244, in > _get_samtools_version raise Exception(message) Exception: Attempting to > use functionality requiring samtools, but it cannot be located on > Galaxy's PATH. > > 4. I restarted the galaxy and the uploaded the bam file. Error: > > Traceback (most recent call last): File > "/galaxy-central/tools/data_source/upload.py", line 425, in <module> > __main__() File "/galaxy-central/tools/data_source/upload.py", line 413, > in __main__ add_file( dataset, registry, json_file, output_path ) File > "/galaxy-central/tools/data_source/upload.py", line 340, in add_file if > link_data_only == 'copy_files' and > datatype.dataset_content_needs_grooming( output_path ): File > "/galaxy-central/lib/galaxy/datatypes/binary.py", line 295, in > dataset_content_needs_grooming version = self._get_samtools_version() > File "/galaxy-central/lib/galaxy/datatypes/binary.py", line 244, in > _get_samtools_version raise Exception(message) Exception: Attempting to > use functionality requiring samtools, but it cannot be located on > Galaxy's PATH. > > > 5. Now, I installed *suite_samtools_1_2 (2015-04-27) devteam* and > updated the packages. File uploaded successfully! > > > > > >> On Aug 14, 2017, at 16:58, Björn Grüning <bjoern.gruen...@gmail.com >> <mailto:bjoern.gruen...@gmail.com>> wrote: >> >> Hi Deepak, >> >> as Peter mentioned the Galaxy Docker container can be used as it is. >> Can you provide the original error message from the TS? >> >> Cheers, >> Bjoern >> >> On 14.08.2017 18:17, Deepak Tanwar wrote: >>> I am using https://hub.docker.com/r/bgruening/galaxy-stable >>> >>> I aded path to the samtools because I was getting error after installing >>> samtools from toolshed. >>> >>> Thank you, >>> Deepak >>> >>>> On Aug 14, 2017, at 12:10, Peter Cock <p.j.a.c...@googlemail.com >>>> <mailto:p.j.a.c...@googlemail.com> >>>> <mailto:p.j.a.c...@googlemail.com>> wrote: >>>> >>>> Galaxy itself uses samtools for many operations, which is different >>>> from when samtools is called as a dependency of a tool run by the >>>> Galaxy user. >>>> >>>> However, the Docker image ought to take care of that - can you >>>> give more details of which Docker image you are using (URL, >>>> version, etc)? >>>> >>>> Thanks, >>>> >>>> Peter >>>> >>>> >>>> On Mon, Aug 14, 2017 at 5:08 PM, Deepak Tanwar <dktan...@hotmail.com >>>> <mailto:dktan...@hotmail.com> >>>> <mailto:dktan...@hotmail.com>> wrote: >>>>> Hello everyone, >>>>> >>>>> I am facing problem in uploading bam files on Galaxy. I am using Docker >>>>> image of Galaxy. >>>>> >>>>> I have installed samtools version 0.1.19 and added it to the path >>>>> /tool_deps/samtools/0.1.19/iuc/package_samtools_0_1_19/c9bd782f5342/bin/samtools >>>>> >>>>> Error: Exception: Attempting to use functionality requiring samtools, >>>>> but it >>>>> cannot be located on Galaxy's PATH. >>>>> >>>>> Thank you, >>>>> Deepak >>>>> >>>>> ___________________________________________________________ >>>>> 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/ >>> >>> >>> >>> ___________________________________________________________ >>> 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/ >>> > ___________________________________________________________ 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/
