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(a)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(a)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(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
>
>