Re: [galaxy-dev] "Failure when preparing job" on blastp
Hi again Peter, John confirmed this was a mistake in the wrappers - for output files .extra_files_path can be shortened to .files_path but this is not yet possible for input files, see discussion on https://github.com/peterjc/galaxy_blast/issues/69 I have updated the BLAST+ wrappers accordingly, and pushed a small update to the Tool Shed: * https://testtoolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/188d2aca045b * https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/b5f1f599d1fb If you are happy to try updating, this should give you all the recent changes like updating to use BLAST+ 2.2.30. Thanks for getting in touch! Peter C. On Tue, Jul 21, 2015 at 7:28 PM, Peter Cock wrote: > Thanks Peter for your very quick reply confirming that > workaround. > > I'll wait to hear from John, as the real fix may be on the > Galaxy side, but we may need to push an update to the > Tool Shed to use the older .extra_files_path form in the > short term. > > Thanks, > > Peter > > On Tue, Jul 21, 2015 at 7:22 PM, Peter van Heusden wrote: >> Previous revision of ncbi_blast_plus works like a charm, thanks. >> >> On 21 July 2015 at 19:57, Peter Cock wrote: >>> >>> Thanks Peter, >>> >>> Yes, you are using the latest release published to >>> the Tool Shed, aka v0.1.03 (internal changes): >>> >>> https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/c16c30e9ad5b >>> >>> I've filed this as an issue on the GitHub repository, >>> https://github.com/peterjc/galaxy_blast/issues/69 >>> >>> If you are also on GitHub we can discuss this there, where >>> I've CC'd John and Bjoern for their thoughts. >>> >>> Something simple you could try now is going back to an older >>> ncbi_blast_plus via the Tool Shed? The previous release >>> 2fe07f50a41e aka v0.1.01 used the alternative form >>> $db_opts.histdb.extra_files_path rather than the current >>> $db_opts.histdb.files_path which appears to be failing. >>> >>> Thanks, >>> >>> Peter >>> >>> On Tue, Jul 21, 2015 at 6:17 PM, Peter van Heusden >>> wrote: >>> > This is release_15.07 (last commit listed is >>> > 39f6730e5f50b54f372b8c1e17d86d8936b5899f) and ncbi_blast_plus >>> > c16c30e9ad5b. >>> > So no, its not an old Galaxy. >>> > >>> > On 21 July 2015 at 17:37, Peter Cock wrote: >>> >> >>> >> Hi Peter v H, >>> >> >>> >> Which version of Galaxy are you running? >>> >> >>> >> Which version of ncbi_blast_tools are you running? (ideally down to >>> >> the ToolShed revision) >>> >> >>> >> My guess is that since this used to be .extra_files_path perhaps your >>> >> Galaxy is too old for .files_path to work? >>> >> >>> >> >>> >> https://github.com/peterjc/galaxy_blast/commit/2bbbf7f361ada20bf1b5bd777fae6e0cb52c4a38 >>> >> >>> >> Thanks, >>> >> >>> >> Peter C. >>> >> >>> >> On Tue, Jul 21, 2015 at 3:08 PM, Peter van Heusden >>> >> wrote: >>> >> > Hi there >>> >> > >>> >> > I'm trying to use the blastp tools from the ncbi_blast_tools, but >>> >> > every >>> >> > time >>> >> > I try and run a job I get the following error: >>> >> > >>> >> > Traceback (most recent call last): >>> >> > File >>> >> > >>> >> > >>> >> > "/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/runners/__init__.py", >>> >> > line 163, in prepare_job >>> >> > job_wrapper.prepare() >>> >> > File >>> >> > >>> >> > >>> >> > "/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/__init__.py", >>> >> > line 859, in prepare >>> >> > self.command_line, self.extra_filenames, >>> >> > self.environment_variables >>> >> > = >>> >> > tool_evaluator.build() >>> >> > File >>> >> > >>> >> > >>> >> > "/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/tools/evaluation.py", >>> >> > line 422, in build >>> >> > raise e >>> >> > NotFound: cannot find 'files_path' while searching for >>> >> > 'db_opts.histdb.files_path' >>> >> > >>> >> > This is happening when expanding the tool template. The BLAST db in >>> >> > in >>> >> > the >>> >> > history (thus the reference to histdb) but why can it not find this >>> >> > attribute? >>> >> > >>> >> > Peter >>> >> > >>> >> > ___ >>> >> > 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] "Failure when preparing job" on blastp
Thanks Peter for your very quick reply confirming that workaround. I'll wait to hear from John, as the real fix may be on the Galaxy side, but we may need to push an update to the Tool Shed to use the older .extra_files_path form in the short term. Thanks, Peter On Tue, Jul 21, 2015 at 7:22 PM, Peter van Heusden wrote: > Previous revision of ncbi_blast_plus works like a charm, thanks. > > On 21 July 2015 at 19:57, Peter Cock wrote: >> >> Thanks Peter, >> >> Yes, you are using the latest release published to >> the Tool Shed, aka v0.1.03 (internal changes): >> >> https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/c16c30e9ad5b >> >> I've filed this as an issue on the GitHub repository, >> https://github.com/peterjc/galaxy_blast/issues/69 >> >> If you are also on GitHub we can discuss this there, where >> I've CC'd John and Bjoern for their thoughts. >> >> Something simple you could try now is going back to an older >> ncbi_blast_plus via the Tool Shed? The previous release >> 2fe07f50a41e aka v0.1.01 used the alternative form >> $db_opts.histdb.extra_files_path rather than the current >> $db_opts.histdb.files_path which appears to be failing. >> >> Thanks, >> >> Peter >> >> On Tue, Jul 21, 2015 at 6:17 PM, Peter van Heusden >> wrote: >> > This is release_15.07 (last commit listed is >> > 39f6730e5f50b54f372b8c1e17d86d8936b5899f) and ncbi_blast_plus >> > c16c30e9ad5b. >> > So no, its not an old Galaxy. >> > >> > On 21 July 2015 at 17:37, Peter Cock wrote: >> >> >> >> Hi Peter v H, >> >> >> >> Which version of Galaxy are you running? >> >> >> >> Which version of ncbi_blast_tools are you running? (ideally down to >> >> the ToolShed revision) >> >> >> >> My guess is that since this used to be .extra_files_path perhaps your >> >> Galaxy is too old for .files_path to work? >> >> >> >> >> >> https://github.com/peterjc/galaxy_blast/commit/2bbbf7f361ada20bf1b5bd777fae6e0cb52c4a38 >> >> >> >> Thanks, >> >> >> >> Peter C. >> >> >> >> On Tue, Jul 21, 2015 at 3:08 PM, Peter van Heusden >> >> wrote: >> >> > Hi there >> >> > >> >> > I'm trying to use the blastp tools from the ncbi_blast_tools, but >> >> > every >> >> > time >> >> > I try and run a job I get the following error: >> >> > >> >> > Traceback (most recent call last): >> >> > File >> >> > >> >> > >> >> > "/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/runners/__init__.py", >> >> > line 163, in prepare_job >> >> > job_wrapper.prepare() >> >> > File >> >> > >> >> > >> >> > "/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/__init__.py", >> >> > line 859, in prepare >> >> > self.command_line, self.extra_filenames, >> >> > self.environment_variables >> >> > = >> >> > tool_evaluator.build() >> >> > File >> >> > >> >> > >> >> > "/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/tools/evaluation.py", >> >> > line 422, in build >> >> > raise e >> >> > NotFound: cannot find 'files_path' while searching for >> >> > 'db_opts.histdb.files_path' >> >> > >> >> > This is happening when expanding the tool template. The BLAST db in >> >> > in >> >> > the >> >> > history (thus the reference to histdb) but why can it not find this >> >> > attribute? >> >> > >> >> > Peter >> >> > >> >> > ___ >> >> > 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/ > > > > ___ > 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] "Failure when preparing job" on blastp
Previous revision of ncbi_blast_plus works like a charm, thanks. On 21 July 2015 at 19:57, Peter Cock wrote: > Thanks Peter, > > Yes, you are using the latest release published to > the Tool Shed, aka v0.1.03 (internal changes): > > https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/c16c30e9ad5b > > I've filed this as an issue on the GitHub repository, > https://github.com/peterjc/galaxy_blast/issues/69 > > If you are also on GitHub we can discuss this there, where > I've CC'd John and Bjoern for their thoughts. > > Something simple you could try now is going back to an older > ncbi_blast_plus via the Tool Shed? The previous release > 2fe07f50a41e aka v0.1.01 used the alternative form > $db_opts.histdb.extra_files_path rather than the current > $db_opts.histdb.files_path which appears to be failing. > > Thanks, > > Peter > > On Tue, Jul 21, 2015 at 6:17 PM, Peter van Heusden > wrote: > > This is release_15.07 (last commit listed is > > 39f6730e5f50b54f372b8c1e17d86d8936b5899f) and ncbi_blast_plus > c16c30e9ad5b. > > So no, its not an old Galaxy. > > > > On 21 July 2015 at 17:37, Peter Cock wrote: > >> > >> Hi Peter v H, > >> > >> Which version of Galaxy are you running? > >> > >> Which version of ncbi_blast_tools are you running? (ideally down to > >> the ToolShed revision) > >> > >> My guess is that since this used to be .extra_files_path perhaps your > >> Galaxy is too old for .files_path to work? > >> > >> > https://github.com/peterjc/galaxy_blast/commit/2bbbf7f361ada20bf1b5bd777fae6e0cb52c4a38 > >> > >> Thanks, > >> > >> Peter C. > >> > >> On Tue, Jul 21, 2015 at 3:08 PM, Peter van Heusden > >> wrote: > >> > Hi there > >> > > >> > I'm trying to use the blastp tools from the ncbi_blast_tools, but > every > >> > time > >> > I try and run a job I get the following error: > >> > > >> > Traceback (most recent call last): > >> > File > >> > > >> > "/net/ > datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/runners/__init__.py > ", > >> > line 163, in prepare_job > >> > job_wrapper.prepare() > >> > File > >> > > >> > "/net/ > datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/__init__.py > ", > >> > line 859, in prepare > >> > self.command_line, self.extra_filenames, > self.environment_variables > >> > = > >> > tool_evaluator.build() > >> > File > >> > > >> > "/net/ > datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/tools/evaluation.py > ", > >> > line 422, in build > >> > raise e > >> > NotFound: cannot find 'files_path' while searching for > >> > 'db_opts.histdb.files_path' > >> > > >> > This is happening when expanding the tool template. The BLAST db in in > >> > the > >> > history (thus the reference to histdb) but why can it not find this > >> > attribute? > >> > > >> > Peter > >> > > >> > ___ > >> > 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/ > ___ 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] "Failure when preparing job" on blastp
Thanks Peter, Yes, you are using the latest release published to the Tool Shed, aka v0.1.03 (internal changes): https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/c16c30e9ad5b I've filed this as an issue on the GitHub repository, https://github.com/peterjc/galaxy_blast/issues/69 If you are also on GitHub we can discuss this there, where I've CC'd John and Bjoern for their thoughts. Something simple you could try now is going back to an older ncbi_blast_plus via the Tool Shed? The previous release 2fe07f50a41e aka v0.1.01 used the alternative form $db_opts.histdb.extra_files_path rather than the current $db_opts.histdb.files_path which appears to be failing. Thanks, Peter On Tue, Jul 21, 2015 at 6:17 PM, Peter van Heusden wrote: > This is release_15.07 (last commit listed is > 39f6730e5f50b54f372b8c1e17d86d8936b5899f) and ncbi_blast_plus c16c30e9ad5b. > So no, its not an old Galaxy. > > On 21 July 2015 at 17:37, Peter Cock wrote: >> >> Hi Peter v H, >> >> Which version of Galaxy are you running? >> >> Which version of ncbi_blast_tools are you running? (ideally down to >> the ToolShed revision) >> >> My guess is that since this used to be .extra_files_path perhaps your >> Galaxy is too old for .files_path to work? >> >> https://github.com/peterjc/galaxy_blast/commit/2bbbf7f361ada20bf1b5bd777fae6e0cb52c4a38 >> >> Thanks, >> >> Peter C. >> >> On Tue, Jul 21, 2015 at 3:08 PM, Peter van Heusden >> wrote: >> > Hi there >> > >> > I'm trying to use the blastp tools from the ncbi_blast_tools, but every >> > time >> > I try and run a job I get the following error: >> > >> > Traceback (most recent call last): >> > File >> > >> > "/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/runners/__init__.py", >> > line 163, in prepare_job >> > job_wrapper.prepare() >> > File >> > >> > "/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/__init__.py", >> > line 859, in prepare >> > self.command_line, self.extra_filenames, self.environment_variables >> > = >> > tool_evaluator.build() >> > File >> > >> > "/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/tools/evaluation.py", >> > line 422, in build >> > raise e >> > NotFound: cannot find 'files_path' while searching for >> > 'db_opts.histdb.files_path' >> > >> > This is happening when expanding the tool template. The BLAST db in in >> > the >> > history (thus the reference to histdb) but why can it not find this >> > attribute? >> > >> > Peter >> > >> > ___ >> > 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/ ___ 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] "Failure when preparing job" on blastp
This is release_15.07 (last commit listed is 39f6730e5f50b54f372b8c1e17d86d8936b5899f) and ncbi_blast_plus c16c30e9ad5b. So no, its not an old Galaxy. On 21 July 2015 at 17:37, Peter Cock wrote: > Hi Peter v H, > > Which version of Galaxy are you running? > > Which version of ncbi_blast_tools are you running? (ideally down to > the ToolShed revision) > > My guess is that since this used to be .extra_files_path perhaps your > Galaxy is too old for .files_path to work? > > https://github.com/peterjc/galaxy_blast/commit/2bbbf7f361ada20bf1b5bd777fae6e0cb52c4a38 > > Thanks, > > Peter C. > > On Tue, Jul 21, 2015 at 3:08 PM, Peter van Heusden > wrote: > > Hi there > > > > I'm trying to use the blastp tools from the ncbi_blast_tools, but every > time > > I try and run a job I get the following error: > > > > Traceback (most recent call last): > > File > > "/net/ > datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/runners/__init__.py > ", > > line 163, in prepare_job > > job_wrapper.prepare() > > File > > "/net/ > datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/__init__.py > ", > > line 859, in prepare > > self.command_line, self.extra_filenames, self.environment_variables = > > tool_evaluator.build() > > File > > "/net/ > datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/tools/evaluation.py > ", > > line 422, in build > > raise e > > NotFound: cannot find 'files_path' while searching for > > 'db_opts.histdb.files_path' > > > > This is happening when expanding the tool template. The BLAST db in in > the > > history (thus the reference to histdb) but why can it not find this > > attribute? > > > > Peter > > > > ___ > > 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] "Failure when preparing job" on blastp
Hi Peter v H, Which version of Galaxy are you running? Which version of ncbi_blast_tools are you running? (ideally down to the ToolShed revision) My guess is that since this used to be .extra_files_path perhaps your Galaxy is too old for .files_path to work? https://github.com/peterjc/galaxy_blast/commit/2bbbf7f361ada20bf1b5bd777fae6e0cb52c4a38 Thanks, Peter C. On Tue, Jul 21, 2015 at 3:08 PM, Peter van Heusden wrote: > Hi there > > I'm trying to use the blastp tools from the ncbi_blast_tools, but every time > I try and run a job I get the following error: > > Traceback (most recent call last): > File > "/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/runners/__init__.py", > line 163, in prepare_job > job_wrapper.prepare() > File > "/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/__init__.py", > line 859, in prepare > self.command_line, self.extra_filenames, self.environment_variables = > tool_evaluator.build() > File > "/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/tools/evaluation.py", > line 422, in build > raise e > NotFound: cannot find 'files_path' while searching for > 'db_opts.histdb.files_path' > > This is happening when expanding the tool template. The BLAST db in in the > history (thus the reference to histdb) but why can it not find this > attribute? > > Peter > > ___ > 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/
