Hi all,
I've updated a Galaxy server with the latest stable distribution "latest_2015.01.13" and now a I got an error:
cannot open galaxy.tools.wrappers.DatasetFilenameWrapper: No such file
The tool has a multiple select field: <param name="input_pdbs" type="data" multiple="true" format="pdb" label="PDB Files" />
On the job details, the select files on the multiple select (there are on my history already), are showed at the Job command line as follow: python /home/alexandre/mestrado/protpred-galaxy/galaxy-dist/tools/analysis/dominance_ranking.py -i [<galaxy.tools.wrappers.DatasetFilenameWrapper object at 0x7f4e1a653290>, <galaxy.tools.wrappers.DatasetFilenameWrapper object at 0x7f4e1a653bd0>, <galaxy.tools.wrappers.DatasetFilenameWrapper object at 0x7f4e1a653d90>, <galaxy.tools.wrappers.DatasetFilenameWrapper object at 0x7f4e1a61de10>]
The command on XML is: <command interpreter="python"> dominance_ranking.py -i $input_pdbs </command>
This tool was working fine before the update.
Any ideas what Is going wrong?
Thanks a lot, Alexandre
Hi Alexandre,
Thanks for reporting this issue. We have committed a fix here https://bitbucket.org/galaxy/galaxy-central/commits/7fd6061e43d5/ and it will be applied to additional releases soon. Please let know if you encounter additional issues.
Thanks for using Galaxy,
Dan
On Jan 14, 2015, at 1:40 PM, Alexandre Defelicibus adefelicibus@gmail.com wrote:
Hi all,
I've updated a Galaxy server with the latest stable distribution "latest_2015.01.13" and now a I got an error: cannot open galaxy.tools.wrappers.DatasetFilenameWrapper: No such file The tool has a multiple select field:
<param name="input_pdbs" type="data" multiple="true" format="pdb" label="PDB Files" />
On the job details, the select files on the multiple select (there are on my history already), are showed at the Job command line as follow: python /home/alexandre/mestrado/protpred-galaxy/galaxy-dist/tools/analysis/dominance_ranking.py -i [<galaxy.tools.wrappers.DatasetFilenameWrapper object at 0x7f4e1a653290>, <galaxy.tools.wrappers.DatasetFilenameWrapper object at 0x7f4e1a653bd0>, <galaxy.tools.wrappers.DatasetFilenameWrapper object at 0x7f4e1a653d90>, <galaxy.tools.wrappers.DatasetFilenameWrapper object at 0x7f4e1a61de10>]
The command on XML is:
<command interpreter="python"> dominance_ranking.py -i $input_pdbs </command>
This tool was working fine before the update.
Any ideas what Is going wrong?
Thanks a lot, Alexandre
-- Alexandre Defelicibus Mestrando em Bioengenharia Programa de Pós-Graduação em Bioengenharia Universidade de São Paulo - USP ___________________________________________________________ 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 Daniel,
Thanks for the answer. How can I update my Galaxy instance with this fix? The fix is on galaxy-central repository and I've cloned the galaxy-dist repository.
Thanks a lot,
Alexandre
2015-01-14 18:29 GMT-02:00 Daniel Blankenberg dan@bx.psu.edu:
Hi Alexandre,
Thanks for reporting this issue. We have committed a fix here https://bitbucket.org/galaxy/galaxy-central/commits/7fd6061e43d5/ and it will be applied to additional releases soon. Please let know if you encounter additional issues.
Thanks for using Galaxy,
Dan
On Jan 14, 2015, at 1:40 PM, Alexandre Defelicibus adefelicibus@gmail.com wrote:
Hi all,
I've updated a Galaxy server with the latest stable distribution "latest_2015.01.13" and now a I got an error:
cannot open galaxy.tools.wrappers.DatasetFilenameWrapper: No such file
The tool has a multiple select field:
<param name="input_pdbs" type="data" multiple="true" format="pdb" label="PDB Files" />
On the job details, the select files on the multiple select (there are on my history already), are showed at the Job command line as follow: python /home/alexandre/mestrado/protpred-galaxy/galaxy-dist/tools/analysis/dominance_ranking.py -i [<galaxy.tools.wrappers.DatasetFilenameWrapper object at 0x7f4e1a653290>, <galaxy.tools.wrappers.DatasetFilenameWrapper object at 0x7f4e1a653bd0>, <galaxy.tools.wrappers.DatasetFilenameWrapper object at 0x7f4e1a653d90>, <galaxy.tools.wrappers.DatasetFilenameWrapper object at 0x7f4e1a61de10>]
The command on XML is:
<command interpreter="python"> dominance_ranking.py -i $input_pdbs </command>
This tool was working fine before the update.
Any ideas what Is going wrong?
Thanks a lot, Alexandre
-- Alexandre Defelicibus Mestrando em Bioengenharia Programa de Pós-Graduação em Bioengenharia Universidade de São Paulo - USP ___________________________________________________________ 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/
Hi Alexandre, the commit seems to be also in galaxy-dist now. Anyway, this command should do the trick:
hg pull -b stable https://bitbucket.org/galaxy/galaxy-central
I'd suggest you to use directly the stable branch of galaxy-central, which usually gets the hotfixes much faster than galaxy-dist. But that's just my personal opinion.
Best, Nicola
Il 15.01.2015 17:32 Alexandre Defelicibus ha scritto:
Hi Daniel, Thanks for the answer.
How can I update
my Galaxy instance with this fix? The fix is on galaxy-central repository and I've cloned the galaxy-dist repository.
Thanks a lot,
Alexandre
2015-01-14 18:29 GMT-02:00 Daniel Blankenberg :
Hi Alexandre,
Thanks for reporting this issue. We have committed a
fix here https://bitbucket.org/galaxy/galaxy-central/commits/7fd6061e43d5/ [3] and it will be applied to additional releases soon. Please let know if you encounter additional issues.
Thanks for using Galaxy, Dan
On Jan 14, 2015, at 1:40 PM, Alexandre Defelicibus wrote:
Hi all, I've updated a Galaxy server with the latest stable
distribution "latest_2015.01.13" and now a I got an error:
cannot open galaxy.tools.wrappers.DatasetFilenameWrapper: No such file
The tool has a multiple select field: On the job
details, the select files on the multiple select (there are on my history already), are showed at the Job command line as follow:
python /home/alexandre/mestrado/protpred-galaxy/galaxy-dist/tools/analysis/dominance_ranking.py -i [, , , ]
The command on XML is:
dominance_ranking.py -i $input_pdbs
This tool was working fine
before the update.
Any ideas what Is going wrong? Thanks a
lot,
Alexandre --
Alexandre Defelicibus Mestrando em
Bioengenharia
Programa de Pós-Graduação em Bioengenharia
Universidade de São Paulo - USP ___________________________________________________________
Please
keep all replies on the list by using "reply all"
in your mail
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and other Galaxy lists,
please use the interface at:
[1]
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--
Alexandre Defelicibus
Mestrando em Bioengenharia Programa de
Pós-Graduação em Bioengenharia
Universidade de São Paulo - USP
--
Nicola Soranzo http://nsoranzo.altervista.org
La mia chiave PGP: http://nsoranzo.altervista.org/key.asc
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