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 <micta...@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 <e...@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.gruen...@gmail.com <mailto:bjoern.gruen...@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/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/
>> >
>> Cheers,
>> Eric
>>
>> --
>> Eric Rasche
>> Programmer II
>>
>> Center for Phage Technology
>> Rm 312A, BioBio
>> Texas A&M University
>> College Station, TX 77843
>> 404-692-2048
>> e...@tamu.edu
>>
>>
>
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