JAFFA installation help

[DANSON WOOI]

Hi 

So far I have had no success installing JAFFA directly based on the instructions since I am on a shared server and do not have root access or privileges. So I tried installing it through anaconda but after the installation the files appear to be named different than if you were to download the package from the github wiki. 

So to take a wild guess I thought the jaffa-assembly script would do what I wanted. Turns out the main problem I having here is that it can't seem to find the reference annotation files. Now since this is anaconda I am not sure which directory to download these files into. Do you think you can guide me on usage of jaffa-assembly? 

here is the error message I get:

echo "Running JAFFA version 2.1" ;             echo "Checking for required data files..." ;             for i in null/hg38_genCode22.fa null/hg38_genCode22.tab /scratch_local/708254.1.short.q/tmp.pLyPvY

R68t/known_fusions.txt null/hg38.fa null/Masked_hg38.1.bt2 null/hg38_genCode22.1.bt2 ;                   do ls $i 2>/dev/null || { echo "CAN'T FIND $i..." ;              echo "PLEASE DOWNLOAD and/or FIX

 PATH... STOPPING NOW" ; exit 1  ; } ; done ;             echo "All looking good" ;             echo "running JAFFA version 2.1.. checks passed" > checks

echo "Running JAFFA version 2.1" ;             echo "Checking for required data files..." ;             for i in null/hg38_genCode22.fa null/hg38_genCode22.tab /scratch_local/708254.1.short.q/tmp.pLyPvY

R68t/known_fusions.txt null/hg38.fa null/Masked_hg38.1.bt2 null/hg38_genCode22.1.bt2 ;                   do ls $i 2>/dev/null || { echo "CAN'T FIND $i..." ;              echo "PLEASE DOWNLOAD and/or FIX

 PATH... STOPPING NOW" ; exit 1  ; } ; done ;             echo "All looking good" ;             echo "running JAFFA version 2.1.. checks passed" > checks

[Nadia Davidson]

Hi, 

Replied at https://github.com/Oshlack/JAFFA/issues/57
Cheers,

Nadia.