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Question: No Kraken database option in galaxy
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gravatar for josef.wagner
2.8 years ago by
josef.wagner • 0
josef.wagner • 0 wrote:

Hello, I am trying to use Kraken in Galaxy. But under "select a kraken database", there is no option available. Could somebody help me to solve this mystery. Kraken does not run, because it ask to verify this parameter i.e. select a kraken database, Thanks, Josef 

 

 
galaxy • 1.2k views
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modified 2.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.8 years ago by josef.wagner • 0
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gravatar for Jennifer Hillman Jackson
2.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This new tool is set up for use right now at the Galaxy public Test instance here: https://test.galaxyproject.org. Promotion of the data to Main (http://usegalaxyorg) is an immediate goal.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k

Dear all,

I've been trying to build a kraken database but We always receive the following error:

Fatal error: Exit code 2 (Error)
--2016-01-27 18:30:47--  ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz
           => “gi_taxid_nucl.dmp.gz”
Resolving ftp.ncbi.nih.gov... 130.14.250.11, 2607:f220:41e:250::7
Connecting to ftp.ncbi.nih.gov|130.14.250.11|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/taxonomy ... done.
==> SIZE gi_taxid_nucl.dmp.gz ... 1360383192
==> PASV ... done.    ==> RETR gi_taxid_nucl.dmp.gz ... done.
Length: 1360383192 (1.3G) (unauthoritative)

     0K .......... .......... .......... .......... ..........  0%  215K 1h42m
    50K .......... .......... .......... .......... ..........  0%  236K 98m21s
   100K .......... .......... .......... .......... ..........  0%  471K 81m14s
   150K .......... .......... .......... .......... ..........  0%  471K 72m41s
   200K .......... .......... .......... 

........

........

Finished processing 252 sequences
python: can't open file '/data_manager/make_json.py': [Errno 2] No such file or directory

I suppose there is a missing link somewhere but I can't find it, even if we have the "/make_json.py" installed under the path=/nfs/staging/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/c3276afba416/data_manager_build_kraken_database/data_manager

Many thanks for any help.

Antonio

ADD REPLY • link written 2.8 years ago by antonio.puertasgallardo • 0

Dear all,

Thanks. I found the "tool_dependency_dir"  parameter in the galaxy.ini file was misconfigured.

now it works.

Antonio

ADD REPLY • link written 2.8 years ago by antonio.puertasgallardo • 0
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