Hi, I supose it is simple misteake but i'm realy close to got mad because dealing with it since friday... so I'm writing to list...
I dont know why galaxy cant find samtools ininstallation dir. It seems that all was done acordingly to admin manual... what I can see after sending bam file is
Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
I thought that galaxy doesntread env.sh file but in log file I have
galaxy.tools DEBUG 2013-11-04 23:07:22,556 Building dependency shell command for dependency 'samtools' galaxy.jobs.runners.local DEBUG 2013-11-04 23:07:22,774 (35) executing: PACKAGE_BASE=/opt/galaxy/galaxy-dist/tools_dependences/samtools/0.1.19; export PACKAGE_BASE; . /opt/galaxy/galaxy-dist/tools_dependences/samtools/0.1.19/env.sh;
all log is in attached file
I have fresh galaxy stable version of galaxy
system centos 6.4 is runing on virtualmachine (vbox) Linux galaxy 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 18:37:12 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
main galaxy instalation dir is /opt/galaxy/galaxy-dist
tools dependency directory in universe_wsgi.ini is tool_dependency_dir = tools_dependences
[galaxy@galaxy galaxy-dist]$ ls -alh /opt/galaxy/galaxy-dist/tools_dependences/samtools/ total 16K drwxrwx--- 4 galaxy galaxy 4.0K Nov 4 22:31 . drwxrwxr-x 3 galaxy galaxy 4.0K Nov 4 22:25 .. drwxrwx--- 3 galaxy galaxy 4.0K Nov 4 23:04 0.1.19 lrwxrwxrwx 1 galaxy galaxy 6 Nov 4 22:31 default -> 0.1.19 drwxrwx--- 6 galaxy galaxy 4.0K Nov 4 22:04 samtools-0.1.19
[galaxy@galaxy galaxy-dist]$ ls -alh /opt/galaxy/galaxy-dist/tools_dependences/samtools/0.1.19/bin/samtools -rwxrwx--- 1 galaxy galaxy 1.5M Nov 4 22:06 /opt/galaxy/galaxy-dist/tools_dependences/samtools/0.1.19/bin/samtools
[galaxy@galaxy galaxy-dist]$ cat /opt/galaxy/galaxy-dist/tools_dependences/samtools/0.1.19/env.sh PATH="/opt/galaxy/galaxy-dist/tools_dependences/samtools/0.1.19/bin:$PATH" export PATH
When I put /opt/galaxy/galaxy-dist/tools_dependences/samtools/0.1.19/bin to /home/galaxy/.bash_profile galaxy CAN see the samtools binaries...
could you tell me what I'm doing wrong?
tj