Hi Edgar,
indeed your bug was fixed long ago, please see http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-td4668186.html


You should really move to the GitHub repository and update to the latest 15.07 or (better) to 15.10 .

Cheers,
Nicola

On 25/01/16 17:09, Fernandez Edgar wrote:

[galaxy@galaxy_sever galaxy-prod]$ hg id -i

f6683935f81a+

*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:*Nicola Soranzo [mailto:nicola.sora...@gmail.com] *On Behalf Of *Nicola Soranzo
*Sent:* January-25-16 12:05 PM
*To:* Fernandez Edgar <edgar.fernan...@umontreal.ca>; Martin Čech <mar...@bx.psu.edu>; galaxy-...@bx.psu.edu
*Subject:* Re: [galaxy-dev] errors installing tool dependencies...

Hi Edgar,
this smells like an old fixed bug, what version of Galaxy are you running?

Cheers,
Nicola

On 25/01/16 14:22, Fernandez Edgar 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>
    <mailto:edgar.fernan...@umontreal.ca>; galaxy-...@bx.psu.edu
    <mailto: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
    athttps://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
    <mailto: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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