Hello Dave, I got interrupted before I could reply to the second suggestion from Jorrit:

Not sure about specifying the absolute path for the tool dependency dir, but I always use it.

using the absolute path of the tool dependency dir had no effect.

Also, my env.sh neither has a #!/bin/bash shebang line, nor quote marks around the tool path.

Removed shebang, quote marks (these are in the wiki example): no effect.

If you are in the hhsuite/default/ dir and source env.sh, can you then run hhblits yourself (as galaxy user, or whoever owns the tools)?

This helped: it looks like I had to specify an additional env variable HHDIR to make it work. So definitely making progress. However, the error was not that the executable was not found, but that HHDIR was missing. I now know I have to use the env.sh BUT: galaxy is not sourcing env.sh. That is my problem. I am confused by your question: if I go with the env.sh solution, I am assuming I do not need to create a 'default' directory and do not need the <requirement> tag. Is this correct? Isabelle On 6/2/14 10:34 AM, "Dave Bouvier" <dave@bx.psu.edu> wrote:

Isabelle,

In order to help track down the cause of this issue, could you provide the output of the following two commands?

ls -lh tool_dependencies/hhsuite/ ls -lh tool_dependencies/hhsuite/default/

--Dave B.

On Mon 02 Jun 2014 01:29:44 PM EDT, Isabelle Phan wrote:

...

I tried <requirements> <requirement type="package">hhsuite</requirement> </requirements>

and that had no effect.

I.

------------------------------

Message: 3 Date: Sat, 31 May 2014 03:51:55 +0200 From: Bj?rn Gr?ning <bjoern.gruening@gmail.com> To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] tool dependencies fail Message-ID: <538935BB.7020905@gmail.com> Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi,

can you try:

<requirements> <requirement type="package">hhsuite</requirement> </requirements>

Hope that helps, sorry for the short answer I'm too tired :) Bjoern

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- Bjoern's suggestion of adding the requirements parent tags around your requirement tag is absolutely needed. - Be sure to restart Galaxy every time you change the tool file (or reload the tool using the admin menu). - Can you share your full tool XML file? - What job runner are you using? If you haven't really played around with job_conf.xml or universe_wsgi.ini it should be just be the local job runner. - Can you verify you do not have a file called dependency_resolvers_conf.xml in your Galaxy root directory - you can break this process if you have mis-defined dependency resolvers. - Finally - can you share Galaxy's log around the time it is trying to run this tool - If Galaxy can find your dependency it should have a line like (except not with samtools): galaxy.tools.deps DEBUG 2014-06-05 08:11:30,739 Building dependency shell command for dependency 'samtools' If Galaxy cannot find your dependency it should have a line like galaxy.tools.deps DEBUG 2014-06-05 08:13:12,777 Building dependency shell command for dependency 'samtools' galaxy.tools.deps WARNING 2014-06-05 08:13:12,777 Failed to resolve dependency on 'samtools', ignoring If neither kind of line can be found - Galaxy is having problems parsing this data from your tool file. If one exists - then Galaxy understands that it should try to find the dependency but cannot - this could mean tool_dependency_dir is wrong, a mis-spelling exists, the symbolic link is wrong, etc.... If you have the top-line but the app is still not on your path (shouldn't be the case since sourcing the file before running Galaxy works) - then there is a problem inside of env.sh. -John On Mon, Jun 2, 2014 at 1:07 PM, Isabelle Phan <isabelle.phan@seattlebiomed.org> wrote:

Galaxy is not sourcing env.sh

I tried sourcing it before restarting galaxy and it worked. So that's the issue.

How do I get galaxy to source env.sh?

$ ls -lh tool_dependencies/hhsuite/ total 8 drwxr-xr-x@ 11 iphan SBRI\Domain Users 374B Jun 2 10:54 2.0.16/ lrwxr-xr-x 1 iphan SBRI\Domain Users 7B Jun 2 10:54 default@ -> 2.0.16/ $ $ ls -lh tool_dependencies/hhsuite/default/ total 784 -rw-r--r--@ 1 iphan SBRI\Domain Users 20K Mar 19 2013 CHANGES -rw-r--r--@ 1 iphan SBRI\Domain Users 36K Mar 19 2013 LICENSE -rw-r--r--@ 1 iphan SBRI\Domain Users 6.0K Mar 19 2013 README drwxr-xr-x@ 10 iphan SBRI\Domain Users 340B May 30 13:18 bin/ -rwxrwxrwx+ 1 iphan SBRI\Domain Users 186B Jun 2 10:54 env.sh* -rw-r--r--@ 1 iphan SBRI\Domain Users 319K Mar 19 2013 hhsuite-userguide.pdf drwxr-xr-x@ 3 iphan SBRI\Domain Users 102B May 30 13:18 include/ drwxr-xr-x@ 6 iphan SBRI\Domain Users 204B May 30 13:20 lib/

thanks,

Isabelle

On 6/2/14 10:50 AM, "Isabelle Phan" <isabelle.phan@seattlebiomed.org> wrote:

...

Hello Dave,

I got interrupted before I could reply to the second suggestion from Jorrit:

...

Not sure about specifying the absolute path for the tool dependency dir, but I always use it.

using the absolute path of the tool dependency dir had no effect.

...

Also, my env.sh neither has a #!/bin/bash shebang line, nor quote marks around the tool path.

Removed shebang, quote marks (these are in the wiki example): no effect.

...

If you are in the hhsuite/default/ dir and source env.sh, can you then run hhblits yourself (as galaxy user, or whoever owns the tools)?

This helped: it looks like I had to specify an additional env variable HHDIR to make it work. So definitely making progress. However, the error was not that the executable was not found, but that HHDIR was missing.

I now know I have to use the env.sh

BUT: galaxy is not sourcing env.sh. That is my problem.

I am confused by your question: if I go with the env.sh solution, I am assuming I do not need to create a 'default' directory and do not need the <requirement> tag. Is this correct?

Isabelle

On 6/2/14 10:34 AM, "Dave Bouvier" <dave@bx.psu.edu> wrote:

...

Isabelle,

In order to help track down the cause of this issue, could you provide the output of the following two commands?

ls -lh tool_dependencies/hhsuite/ ls -lh tool_dependencies/hhsuite/default/

--Dave B.

On Mon 02 Jun 2014 01:29:44 PM EDT, Isabelle Phan wrote:

...

I tried <requirements> <requirement type="package">hhsuite</requirement> </requirements>

and that had no effect.

I.

------------------------------

Message: 3 Date: Sat, 31 May 2014 03:51:55 +0200 From: Bj?rn Gr?ning <bjoern.gruening@gmail.com> To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] tool dependencies fail Message-ID: <538935BB.7020905@gmail.com> Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi,

can you try:

<requirements> <requirement type="package">hhsuite</requirement> </requirements>

Hope that helps, sorry for the short answer I'm too tired :) Bjoern

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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: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/