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 <d...@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.c...@googlemail.com <mailto:p.j.a.c...@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-...@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-iuc
___________________________________________________________
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/

Reply via email to