"Failure when preparing job" on blastp
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
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/2bbbf7f361ada20bf1b5bd777fae6... Thanks, Peter C. On Tue, Jul 21, 2015 at 3:08 PM, Peter van Heusden <pvh@sanbi.ac.za> 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
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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 <p.j.a.cock@googlemail.com> 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/2bbbf7f361ada20bf1b5bd777fae6...
Thanks,
Peter C.
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
On Tue, Jul 21, 2015 at 3:08 PM, Peter van Heusden <pvh@sanbi.ac.za> wrote: the
history (thus the reference to histdb) but why can it not find this attribute?
Peter
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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 <pvh@sanbi.ac.za> 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 <p.j.a.cock@googlemail.com> 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/2bbbf7f361ada20bf1b5bd777fae6...
Thanks,
Peter C.
On Tue, Jul 21, 2015 at 3:08 PM, Peter van Heusden <pvh@sanbi.ac.za> 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
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Previous revision of ncbi_blast_plus works like a charm, thanks. On 21 July 2015 at 19:57, Peter Cock <p.j.a.cock@googlemail.com> 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 <pvh@sanbi.ac.za> 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 <p.j.a.cock@googlemail.com> 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/2bbbf7f361ada20bf1b5bd777fae6...
Thanks,
Peter C.
On Tue, Jul 21, 2015 at 3:08 PM, Peter van Heusden <pvh@sanbi.ac.za> 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
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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/
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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 <pvh@sanbi.ac.za> wrote:
Previous revision of ncbi_blast_plus works like a charm, thanks.
On 21 July 2015 at 19:57, Peter Cock <p.j.a.cock@googlemail.com> 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 <pvh@sanbi.ac.za> 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 <p.j.a.cock@googlemail.com> 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/2bbbf7f361ada20bf1b5bd777fae6...
Thanks,
Peter C.
On Tue, Jul 21, 2015 at 3:08 PM, Peter van Heusden <pvh@sanbi.ac.za> 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/
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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 <p.j.a.cock@googlemail.com> 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 <pvh@sanbi.ac.za> wrote:
Previous revision of ncbi_blast_plus works like a charm, thanks.
On 21 July 2015 at 19:57, Peter Cock <p.j.a.cock@googlemail.com> 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 <pvh@sanbi.ac.za> 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 <p.j.a.cock@googlemail.com> 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/2bbbf7f361ada20bf1b5bd777fae6...
Thanks,
Peter C.
On Tue, Jul 21, 2015 at 3:08 PM, Peter van Heusden <pvh@sanbi.ac.za> 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/
participants (2)
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Peter Cock -
Peter van Heusden