Still need to remove @ from paths in perl script?

[David]

Hi,
AFAIK, the only way to correct this is going to the actual code, as it seems is hard-wired. The Galaxy team should take a more detailed look.

There are at least 4 other issues related to this specific bug of “@” in paths here at Galaxy Help:

MAKER failed [qrsh] <defunct>

I have an issue with MAKER. When a launch maker, the jobs never end and use < 1 cpu. After looking on the node, i see that qrsh failed : [qrsh] Any help would be appreciated. [galaxy@node11 ~]$ ps aux | grep galaxy galaxy 32367 0.0 0.0 107088 1548 ? Ss 17:51 0:00 /bin/bash /media/vol2/home/galaxy/galaxy/database/jobs_directory/000/56/galaxy_56.sh galaxy 32386 0.1 0.0 106192 1608 ? S 17:51 0:00 /bin/bash /media/vol2/home/galaxy/galaxy/database/jobs_dire…

this first one is about maker too (V 2.31.10):

Possible unintended interpolation of @2 in string at /media/vol2/home/galaxy/galaxy/database/dependencies/_conda/envs/__maker@2.31.10/bin/../lib/5.26.2/x86_64-linux-thread-multi/Config_heavy.pl line 260.
  Possible precedence issue with control flow operator at /media/vol2/home/galaxy/galaxy/database/dependencies/_conda/envs/__maker@2.31.10/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
  error: executing task of job 1007802 failed: execution daemon on host "node11" didn't accept task

The others :

How to view Kraken2 Results in Krona?

Hi , I am trying to install kraken2 databases through data manger. Its giving me an URL error to download the databases. Can you please check if the URL provided is correct?. here is the error: Fatal error: Exit code 1 () Possible unintended interpolation of @2 in string at /dep/_conda/envs/__kraken2@2.0.7_beta/bin/kraken2 line 16. Traceback (most recent call last): File “/data/shed_tools/testtoolshed.g2.bx.psu.edu/repos/dfornika/data_manager_build_kraken2_database/65cbfb5e6f65/data_manager…

Error with Trinity De Novo Assembly in GVL 4.4.0 install

We’ve been experiencing persistent error pasted below with our lab’s cloud-based installation of the Galaxy suite via the Genomics Virtual Laboratory 4.4.0. Specifically, whenever we attempt a Trinity de novo assembly of a collection of Illumina TruSeq stranded mRNA paired end reads, we get the errors below. We’ve had no problems with these same data sets when using other tools like HiSat2 and StringTie. We’ve poked around in the “manage tools” and “manage dependencies” area of the Galaxy Ad…

Kraken2 tool error

I see that there is an datamangers for kraken2 to install Minikraken2. Now I am able to install Minikraken2 but it doent contain all the required files to finish the job. taxo.k2d file is missing. Fatal error: Exit code 2 () Possible unintended interpolation of @2 in string at /dep/_conda/envs/__kraken2@2.0.7_beta/bin/kraken2 line 16. kraken2: database ("/tool/tool-data/kraken2_databases/2019-05-07T122927Z_minikraken2_v2_8GB") does not contain necessary file taxo.k2d Thanks, Jayanthi