Hi all, Thank you for all response. I setup galaxy, postgresql and proFTPd from scratch and installed all tools. Now everything it is working.
Thank you in advance.
Best wishes,
Mic
On Tue, Nov 17, 2015 at 2:23 PM, Mic mictadlo@gmail.com wrote:
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@tamu.edu 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@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/rgFas...
> <http://toolshed.g2.bx.psu.edu/repos/devteam/fastqc/2d094334f61e/fastqc/rgFas...
", > line 157, in <module> assert
os.path.isfile(opts.executable),'##rgFastQC.py
> error - cannot find executable %s' % opts.executableAssertionError:
> ##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 402:21
> .drwxrwxr-x 3 lorencm lorencm 4.0K Nov 4 02:21 ..drwxrwxr-x 2lorencm
> 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-- 1lorencm
> 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@tamu.edu