Hello, I installed FastQC (~/shed_tools/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...;, 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/

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/

HI Eric, I compared your two files to mine ones and notices that *FASTQC_ROOT_DIR* was missing, but after I adding it, I still get the same error. cat ~/galaxy/tool_dependency/FastQC/0.11.2/devteam/fastqc/2d094334f61e/env.sh if [ -f /home/lorencm/galaxy/tool_dependency/FastQC/0.11.2/devteam/package_fastqc_0_11_2/4b65f6e39cb0/env.sh ] ; then . /home/lorencm/galaxy/tool_dependency/FastQC/0.11.2/devteam/package_fastqc_0_11_2/4b65f6e39cb0/env.sh ; fi cat ~/galaxy/tool_dependency/FastQC/0.11.2/devteam/package_fastqc_0_11_2/4b65f6e39cb0/env.sh PATH=/home/lorencm/galaxy/tool_dependency/FastQC/0.11.2/devteam/package_fastqc_0_11_2/4b65f6e39cb0:$PATH; export PATH FASTQC_JAR_PATH=/home/lorencm/galaxy/tool_dependency/FastQC/0.11.2/devteam/package_fastqc_0_11_2/4b65f6e39cb0; export FASTQC_JAR_PATH *FASTQC_ROOT_DIR=/home/lorencm/galaxy/tool_dependency/FastQC/0.11.2/devteam/package_fastqc_0_11_2/4b65f6e39cb0; export FASTQC_ROOT_DIR* I would have removed fastqc already and installed it again, but after I migrated to Postgresql, I am not able to change my API key to previous ones. Do you have any idea how can I change it in Postrgresql manually? What am I missing? Thank you in advance. Mic On Tue, Nov 17, 2015 at 1:16 PM, Eric Rasche <esr(a)tamu.edu&gt; wrote: > /##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 > >