/##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.gruening@gmail.com <mailto:bjoern.gruening@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*>
Cheers,> > /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:
> http://galaxyproject.org/search/mailinglists/
>
Eric
--
Eric Rasche
Programmer II
Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048
esr@tamu.edu