That was my second guess, I wasn't sure whether it should create that dir
structure. Are you installing this package at this revision? And what
system are you installing it on?

https://toolshed.g2.bx.psu.edu/view/iuc/package_bowtie_2_2_6/0d9cd7487cc9

M.

On Mon, Jan 25, 2016 at 11:17 AM Fernandez Edgar <
edgar.fernan...@umontreal.ca> wrote:

> No wait my mistake: the path doesn’t exists:
>
>
> [Errno 2] No such file or directory: 
> '/home/galaxy/galaxy-prod/database/tmp/tmp-toolshed-mtdb6vbEI/bowtie2-2.2.6/bowtie2-2.2.6/'
>
> Because you have twice "bowtie2-2.2.6" in the full path…
>
> Is that normal?
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la Communication
>
> *Université de Montréal*
>
>
>
> PAVILLON ROGER-GAUDRY, bureau X-210
>
> (  Bur. : *1-514-343-6111 poste 16568*
>
>
>
>
>
> *From:* Fernandez Edgar
> *Sent:* January-25-16 11:11 AM
> *To:* 'Martin Čech' <mar...@bx.psu.edu>; galaxy-...@bx.psu.edu
> *Subject:* RE: [galaxy-dev] errors installing tool dependencies...
>
>
>
> Hello Martin.
>
>
>
> I changed the setting “new_file_path” like you said and the same error
> occurs (with the full path obviously).
>
> I check that the full path exists. And is rwx for the galaxy user.
>
> Any other ideas I could try?
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la Communication
>
> *Université de Montréal*
>
>
>
> PAVILLON ROGER-GAUDRY, bureau X-210
>
> (  Bur. : *1-514-343-6111 poste 16568*
>
>
>
>
>
> *From:* Martin Čech [mailto:mar...@bx.psu.edu <mar...@bx.psu.edu>]
> *Sent:* January-25-16 9:33 AM
>
>
> *To:* Fernandez Edgar <edgar.fernan...@umontreal.ca>;
> galaxy-...@bx.psu.edu
> *Subject:* Re: [galaxy-dev] errors installing tool dependencies...
>
>
>
> Hi Edgar,
>
>
>
> I am not sure about this one. Please try setting 'new_file_path' in your
> galaxy.ini to an absolute path, try again and check whether something
> changes.
>
>
>
> Martin
>
>
>
> On Mon, Jan 25, 2016 at 9:23 AM Fernandez Edgar <
> edgar.fernan...@umontreal.ca> wrote:
>
> Hello Martin,
>
>
>
> Thank you!
>
> Your instructions for my problem with Perl package worked.
>
> For the URL of hmmer, it is wrong and I will report it like you suggested
> it.
>
>
>
> Finally, a new error occurred for bowtie.
>
> Would you please take a look?
>
>
>
> My Sincere Salutations,
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la Communication
>
> *Université de Montréal*
>
>
>
> PAVILLON ROGER-GAUDRY, bureau X-210
>
> (  Bur. : *1-514-343-6111 poste 16568*
>
>
>
>
>
> *From:* Martin Čech [mailto:mar...@bx.psu.edu]
> *Sent:* January-22-16 2:34 PM
> *To:* Fernandez Edgar <edgar.fernan...@umontreal.ca>;
> galaxy-...@bx.psu.edu
> *Subject:* Re: [galaxy-dev] errors installing tool dependencies...
>
>
>
> Hi Edgar,
>
> for the package_perl issue please try installing updates to the
> dependencies (package_gnu_coreutils and package_perl in their respective
> versions) and then return to this screen and click the 'repository action'
> button and then 'manage dependencies' from the menu. Uninstall both
> dependencies (gnu_coreutil and perl) and then install them again.
>
> That should pick up the newest versions and you should be set.
>
>
>
> Regarding the hmmer that is a more prosaic problem, at the time of the
> installation the software was not available at the given URL. Check the
> machine's internet connection and if it is ok try downloading the file
> manually. If it succeeds the problem might have been on their side and is
> ok now. If it does not the problem can still be on their side and in that
> case either wait a bit and try again or report the issue at
> https://github.com/galaxyproject/tools-iuc/issues
>
>
>
> thank you for using Galaxy.
>
>
>
> Martin
>
> On Fri, Jan 22, 2016 at 2:24 PM Fernandez Edgar <
> edgar.fernan...@umontreal.ca> wrote:
>
> Hello guys,
>
>
>
> Happy new year everyone!
>
> Wish you all the best!
>
>
>
> I have a couple of small problems I’ve attached as pictures…
>
> Can you please help me?
>
>
>
> INFO: My galaxy installation and database is updated today!
>
>
>
> My sincere salutations,
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la Communication
>
> *Université de Montréal*
>
>
>
> PAVILLON ROGER-GAUDRY, bureau X-210
>
> (  Bur. : *1-514-343-6111 poste 16568         *
>
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