Re: [galaxy-dev] rgFastQC.py error - cannot find executable /fastqc

/##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(a)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*> > > /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/rg... > > > > < http://toolshed.g2.bx.psu.edu/repos/devteam/fastqc/2d094334f61e/fastqc/rg... >", > > 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/ > Cheers, Eric -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843 404-692-2048 esr(a)tamu.edu