Peter, From what I've been able to determine, samtools' failure was due to an error in the testing environment startup process, which in turn caused errors in a number of tool dependency packages. I've fixed the initial error, and the next test run should result in a successful samtools installation. --Dave B. On Mon 21 Apr 2014 06:52:50 AM EDT, Peter Cock wrote:

Hi all,

This samtools dependency error is now showing for all my Test ToolShed repositories using the samtools package:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler

Looking at the package itself, it looks like a ncurses (or curses) library dependency problem - perhaps something changed on the ToolShed server configuration?

http://testtoolshed.g2.bx.psu.edu/view/iuc/package_samtools_0_1_19

Regards,

Peter

On Wed, Apr 16, 2014 at 11:43 AM, Peter Cock <p.j.a.cock@googlemail.com <mailto:p.j.a.cock@googlemail.com>> wrote:

Hi all,

I'm working on a new wrapper for "samtools depad" (which I have been using with MIRA v4 output), now on the Test ToolShed:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad

The unit tests work for me locally and via TravisCI.

The nightly ToolShed tests are failing - something seems to have gone wrong with the samtools dependency ("status Error") event though the samtools package is listed as a successful installation. Odd...

Any thoughts?

Thanks,

Peter

--

Automated tool test results

Automated test environment *Time tested:* 2014-04-16 05:07:24 *System:* Linux 3.8.0-30-generic *Architecture:* x86_64 *Python version:* 2.7.4 *Galaxy revision:* 13078:6f698dec5895 *Galaxy database version:* 118 *Tool shed revision:* 13018:e20408b06d65 *Tool shed database version:* 22 *Tool shed mercurial version:* 2.2.3

Installation errors Tool dependencies Type Name Version samtools package 0.1.19 Error This tool dependency's required tool dependency samtools version 0.1.19 has status Error.

Successful installations Repository dependencies/- installation of these additional repositories is required/ Tool shed Name Owner Changeset revision testtoolshed.g2.bx.psu.edu <http://testtoolshed.g2.bx.psu.edu> package_samtools_0_1_19 iuc 36aa94676939

_______________________________________________ galaxy-iuc mailing list galaxy-iuc@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-iuc

The two options I normally use for that are the "Repository dependency definitions" and "Tool dependency definitions" links under the "Valid Galaxy Utilities" heading in the left panel, which provide an overview of all dependencies of the relevant type. --Dave B. On Mon 21 Apr 2014 09:39:51 AM EDT, Peter Cock wrote:

Thanks Dave,

On a slight tangent, is there a way in the ToolShed to see what other repositories use a given repository as a dependency?

e.g. From http://testtoolshed.g2.bx.psu.edu/view/iuc/package_samtools_0_1_19 it there any way to see what uses samtools 0.1.19?

Cheers,

Peter

On Mon, Apr 21, 2014 at 2:24 PM, Dave Bouvier <dave@bx.psu.edu> wrote:

...

Peter,

From what I've been able to determine, samtools' failure was due to an error in the testing environment startup process, which in turn caused errors in a number of tool dependency packages. I've fixed the initial error, and the next test run should result in a successful samtools installation.

--Dave B.

On Mon 21 Apr 2014 06:52:50 AM EDT, Peter Cock wrote:

...

Hi all,

This samtools dependency error is now showing for all my Test ToolShed repositories using the samtools package:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler

Looking at the package itself, it looks like a ncurses (or curses) library dependency problem - perhaps something changed on the ToolShed server configuration?

http://testtoolshed.g2.bx.psu.edu/view/iuc/package_samtools_0_1_19

Regards,

Peter

On Wed, Apr 16, 2014 at 11:43 AM, Peter Cock <p.j.a.cock@googlemail.com <mailto:p.j.a.cock@googlemail.com>> wrote:

Hi all,

I'm working on a new wrapper for "samtools depad" (which I have been using with MIRA v4 output), now on the Test ToolShed:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad

The unit tests work for me locally and via TravisCI.

The nightly ToolShed tests are failing - something seems to have gone wrong with the samtools dependency ("status Error") event though the samtools package is listed as a successful installation. Odd...

Any thoughts?

Thanks,

Peter

--

Automated tool test results

Automated test environment *Time tested:* 2014-04-16 05:07:24 *System:* Linux 3.8.0-30-generic *Architecture:* x86_64 *Python version:* 2.7.4 *Galaxy revision:* 13078:6f698dec5895 *Galaxy database version:* 118 *Tool shed revision:* 13018:e20408b06d65 *Tool shed database version:* 22 *Tool shed mercurial version:* 2.2.3

Installation errors Tool dependencies Type Name Version samtools package 0.1.19 Error This tool dependency's required tool dependency samtools version 0.1.19 has status Error.

Successful installations Repository dependencies/- installation of these additional repositories is required/

Tool shed Name Owner Changeset revision testtoolshed.g2.bx.psu.edu <http://testtoolshed.g2.bx.psu.edu> package_samtools_0_1_19 iuc 36aa94676939

_______________________________________________ galaxy-iuc mailing list galaxy-iuc@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-iuc

Peter, Based on the latest test run, and my own investigations, it would appear that the samtools compilation process is looking in the wrong include path for ncurses/ncurses_dll.h. My recommendation would be to replace the following: -I$NCURSES_INCLUDE_PATH/ncurses/ with -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH in the shell_command for package_samtools_0_1_19's tool_dependencies.xml that starts with: sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*| --Dave B. On Mon 28 Apr 2014 12:13:27 PM EDT, Peter Cock wrote:

Hi Dave,

This problem persists (or has reoccured),

This tool dependency's required tool dependency samtools version 0.1.19 has status Error.

Did you discover anymore last week? Sorry for the lag in my reply, I busy with other things.

Thanks,

Peter

On Mon, Apr 21, 2014 at 2:24 PM, Dave Bouvier <dave@bx.psu.edu> wrote:

...

Peter,

From what I've been able to determine, samtools' failure was due to an error in the testing environment startup process, which in turn caused errors in a number of tool dependency packages. I've fixed the initial error, and the next test run should result in a successful samtools installation.

--Dave B.

On Mon 21 Apr 2014 06:52:50 AM EDT, Peter Cock wrote:

...

Hi all,

This samtools dependency error is now showing for all my Test ToolShed repositories using the samtools package:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler

Looking at the package itself, it looks like a ncurses (or curses) library dependency problem - perhaps something changed on the ToolShed server configuration?

http://testtoolshed.g2.bx.psu.edu/view/iuc/package_samtools_0_1_19

Regards,

Peter

On Wed, Apr 16, 2014 at 11:43 AM, Peter Cock <p.j.a.cock@googlemail.com <mailto:p.j.a.cock@googlemail.com>> wrote:

Hi all,

I'm working on a new wrapper for "samtools depad" (which I have been using with MIRA v4 output), now on the Test ToolShed:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad

The unit tests work for me locally and via TravisCI.

The nightly ToolShed tests are failing - something seems to have gone wrong with the samtools dependency ("status Error") event though the samtools package is listed as a successful installation. Odd...

Any thoughts?

Thanks,

Peter

--

Automated tool test results

Automated test environment *Time tested:* 2014-04-16 05:07:24 *System:* Linux 3.8.0-30-generic *Architecture:* x86_64 *Python version:* 2.7.4 *Galaxy revision:* 13078:6f698dec5895 *Galaxy database version:* 118 *Tool shed revision:* 13018:e20408b06d65 *Tool shed database version:* 22 *Tool shed mercurial version:* 2.2.3

Installation errors Tool dependencies Type Name Version samtools package 0.1.19 Error This tool dependency's required tool dependency samtools version 0.1.19 has status Error.

Successful installations Repository dependencies/- installation of these additional repositories is required/

Tool shed Name Owner Changeset revision testtoolshed.g2.bx.psu.edu <http://testtoolshed.g2.bx.psu.edu> package_samtools_0_1_19 iuc 36aa94676939

_______________________________________________ galaxy-iuc mailing list galaxy-iuc@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-iuc

Hi, I updated the test and the tool shed accordingly to Dave suggestion. I'm just wondering, the TS tests were passing with the old version, anything I should worry about? :) Thanks and sorry for the inconvenience! Bjoern Am 29.04.2014 16:07, schrieb Peter Cock:

On Tue, Apr 29, 2014 at 2:59 PM, Dave Bouvier <dave@bx.psu.edu> wrote:

...

Peter,

Based on the latest test run, and my own investigations, it would appear that the samtools compilation process is looking in the wrong include path for ncurses/ncurses_dll.h. My recommendation would be to replace the following:

-I$NCURSES_INCLUDE_PATH/ncurses/

with

-I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH

in the shell_command for package_samtools_0_1_19's tool_dependencies.xml that starts with: sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|

--Dave B.

Thanks Dave,

That sounds like it would be more robust to subtle server changes.

I see Bjoern has been working on this today with a slightly different change - I'll leave this in his capable hands:

https://github.com/bgruening/galaxytools/commits/master/orphan_tool_dependen...

Regards,

Peter