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:marten@bx.psu.edu] Sent: January-22-16 2:34 PM To: Fernandez Edgar <edgar.fernandez@umontreal.ca>; galaxy-dev@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.fernandez@umontreal.ca<mailto:edgar.fernandez@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 ___________________________________________________________ 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/

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:marten@bx.psu.edu] Sent: January-25-16 9:33 AM To: Fernandez Edgar <edgar.fernandez@umontreal.ca>; galaxy-dev@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.fernandez@umontreal.ca<mailto:edgar.fernandez@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:marten@bx.psu.edu<mailto:marten@bx.psu.edu>] Sent: January-22-16 2:34 PM To: Fernandez Edgar <edgar.fernandez@umontreal.ca<mailto:edgar.fernandez@umontreal.ca>>; galaxy-dev@bx.psu.edu<mailto:galaxy-dev@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.fernandez@umontreal.ca<mailto:edgar.fernandez@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 ___________________________________________________________ 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/

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.fernandez@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' <marten@bx.psu.edu>; galaxy-dev@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:marten@bx.psu.edu <marten@bx.psu.edu>] *Sent:* January-25-16 9:33 AM

*To:* Fernandez Edgar <edgar.fernandez@umontreal.ca>; galaxy-dev@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.fernandez@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:marten@bx.psu.edu] *Sent:* January-22-16 2:34 PM *To:* Fernandez Edgar <edgar.fernandez@umontreal.ca>; galaxy-dev@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.fernandez@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 *

___________________________________________________________ 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/