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bcgsc / transabyss

de novo assembly of RNA-seq data using ABySS
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awk files not found #16

Closed 54mu closed 5 years ago

54mu commented 5 years ago

Hi, I installed transabyss via bioconda, within the Oyster River Protocol, after working a first time, now i get a missing files error:

Found Trans-ABySS directory at: 
/mnt/DATA/Software/Oyster_River_Protocol/software/anaconda/install/envs/orp/lib/python3.6/site-packages
Found Trans-ABySS `bin` directory at: /mnt/DATA/Software/Oyster_River_Protocol/software/anaconda/install/envs/orp/lib/python3.6/site-packages/bin
No such file: skip_psl_self.awk
No such file: skip_psl_self_ss.awk
Found `abyss-pe' at /mnt/DATA/Software/Oyster_River_Protocol/software/anaconda/install/envs/orp/bin/abyss-pe
Found `MergeContigs' at /mnt/DATA/Software/Oyster_River_Protocol/software/anaconda/install/envs/orp/bin/MergeContigs
Found `abyss-filtergraph' at /mnt/DATA/Software/Oyster_River_Protocol/software/anaconda/install/envs/orp/bin/abyss-filtergraph
Found `abyss-junction' at /mnt/DATA/Software/Oyster_River_Protocol/software/anaconda/install/envs/orp/bin/abyss-junction
Found `blat' at /mnt/DATA/Software/Oyster_River_Protocol/software/anaconda/install/envs/orp/bin/blat
Found `abyss-map' at /mnt/DATA/Software/Oyster_River_Protocol/software/anaconda/install/envs/orp/bin/abyss-map
ERROR: Your environment is not sufficient to run Trans-ABySS. Please check the missing executables, scripts, or directories.

do you have any insight? Thanks

EDIT: there was a conflicting version installed, re-exporting path fixed the essue

sjackman commented 5 years ago

Please surround copied-and-pasted logs with triple back ticks. See GitHub Help / Quoting Code.

sjackman commented 5 years ago

Glad to hear that you found a fix.