/##rgFastQC.py error - cannot find executable /fastqc
/

That specific error is caused by the environment variable 
$FASTQC_JAR_PATH/$FASQTC_ROOT_DIR being empty. I suggest checking to see that 
all the correct environment files are loadable. I had this issue recently where 
I moved my galaxy installation and FastQC failed exactly like that.

Konsole output
# cat tool_dependencies/FastQC/0.11.2/devteam/fastqc/0b201de108b9/env.sh  
if [ -f 
/galaxy/tool_dependencies/FastQC/0.11.2/devteam/package_fastqc_0_11_2/4b65f6e39cb0/env.sh
 ] ;
  then . 
/galaxy/tool_dependencies/FastQC/0.11.2/devteam/package_fastqc_0_11_2/4b65f6e39cb0/env.sh
 ;
fi

In that file, the env.sh file mentioned should be accessible. When I moved my 
galaxy, the env.sh file originally had a "/home/galaxy" prefixing it and was 
inaccessible causing a failure to load. You may have that, or some other issue 
that's causing the file to be inaccessible and the environment variables 
contained within to not be loaded:

Konsole output
# cat 
/galaxy/tool_dependencies/FastQC/0.11.2/devteam/package_fastqc_0_11_2/4b65f6e39cb0/env.sh
PATH=/galaxy/tool_dependencies/FastQC/0.11.2/devteam/package_fastqc_0_11_2/4b65f6e39cb0:$PATH;
 export PATH
FASTQC_JAR_PATH=/galaxy/tool_dependencies/FastQC/0.11.2/devteam/package_fastqc_0_11_2/4b65f6e39cb0;
 export FASTQC_JAR_PATH
FASTQC_ROOT_DIR=/galaxy/tool_dependencies/FastQC/0.11.2/devteam/package_fastqc_0_11_2/4b65f6e39cb0;
 export FASTQC_ROOT_DIR


On 11/16/2015 09:10 PM, Mic wrote:
> Hi Bjoern,
> Yes, I do:
>
> > java -version
> java version "1.7.0_85"
> OpenJDK Runtime Environment (IcedTea 2.6.1) (7u85-2.6.1-5ubuntu0.14.04.1)
> OpenJDK 64-Bit Server VM (build 24.85-b03, mixed mode)
>
> Can it be related that my API key has change while migrating to
> Postgresql? I tried to put it back the old one in /galaxy.ini/, but
> Galaxy does not pick it from /master_api_key/.
>
> Thank you in advance.
>
> Mic
>
>
>
> On Tue, Nov 17, 2015 at 12:28 PM, Björn Grüning
> <bjoern.gruen...@gmail.com <mailto:bjoern.gruen...@gmail.com>> wrote:
>
>     Hi Mic,
>
>     do you have Java installed?
>
>     cheers,
>     Bjoern
>
>     Am 17.11.2015 um 02:05 schrieb Mic:
>     > Hello,
>     > I installed FastQC
>     (~/shed_tools/toolshed.g2.bx.psu.edu/repos/*devteam*
>     <http://toolshed.g2.bx.psu.edu/repos/*devteam*>
>     > /fastqc/*2d094334f61e*/
>     >
>     > *FastQC ).*
>     > However, I got the following error while running it:
>     >
>     >
>     > *Fatal error: Exit code 1 () Traceback (most recent call last): File
>     >
>     
> "/home/lorencm/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/2d094334f61e/fastqc/rgFastQC.py
>     
> <http://toolshed.g2.bx.psu.edu/repos/devteam/fastqc/2d094334f61e/fastqc/rgFastQC.py>
>     >
>     
> <http://toolshed.g2.bx.psu.edu/repos/devteam/fastqc/2d094334f61e/fastqc/rgFastQC.py>",
>     > line 157, in <module> assert 
> os.path.isfile(opts.executable),'##rgFastQC.py
>     > error - cannot find executable %s' % opts.executable AssertionError:
>     > ##rgFastQC.py error - cannot find executable /fastqc*
>     >
>     > The Fastqc package seems to be correctly installed:
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     
> *~/galaxy/tool_dependency/FastQC/0.11.2/devteam/package_fastqc_0_11_2/4b65f6e39cb0
>     >> ls -1 -ahltotal 824Kdrwxrwxr-x 8 lorencm lorencm 4.0K Nov  4 02:21
>     > .drwxrwxr-x 3 lorencm lorencm 4.0K Nov  4 02:21 ..drwxrwxr-x 2 lorencm
>     > lorencm 4.0K Nov  4 02:21 Configuration-rwxrwxr-x 1 lorencm
>     lorencm  251
>     > Nov  4 02:21 env.sh-rwxr-xr-x 1 lorencm lorencm  13K Nov  4 02:21
>     > fastqc-rw-rw-r-- 1 lorencm lorencm 2.2K Nov  4 02:21
>     > fastqc_icon.icodrwxrwxr-x 5 lorencm lorencm 4.0K Nov  4 02:21
>     > Help-rw-rw-r-- 1 lorencm lorencm 5.5K Nov  4 02:21
>     INSTALL.txt-rw-rw-r-- 1
>     > lorencm lorencm  49K Nov  4 02:21 jbzip2-0.9.jar-rw-rw-r-- 1 lorencm
>     > lorencm  35K Nov  4 02:21 LICENSE.txtdrwxrwxr-x 3 lorencm lorencm
>     4.0K Nov
>     > 4 02:21 netdrwxrwxr-x 3 lorencm lorencm 4.0K Nov  4 02:21
>     org-rw-rw-r-- 1
>     > lorencm lorencm 2.1K Nov  4 02:21 README.txt-rw-rw-r-- 1 lorencm
>     lorencm
>     > 32K Nov  4 02:21 RELEASE_NOTES.txt-rw-rw-r-- 1 lorencm lorencm
>     101 Nov  4
>     > 02:21 run_fastqc.bat-rw-rw-r-- 1 lorencm lorencm 630K Nov  4 02:21
>     > sam-1.103.jardrwxrwxr-x 3 lorencm lorencm 4.0K Nov  4 02:21
>     > Templatesdrwxrwxr-x 3 lorencm lorencm 4.0K Nov  4 02:21 uk*
>     > What do I miss out?
>     >
>     > Thank you in advance.
>     >
>     > Mic
>     >
>     >
>     >
>     > ___________________________________________________________
>     > 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/
>     >
>
>
>
>
> ___________________________________________________________
> 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:
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>
Cheers,
Eric

-- 
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048
e...@tamu.edu

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