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ndaniel / fusioncatcher

Finder of Somatic Fusion Genes in RNA-seq data
GNU General Public License v3.0
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Change --link hard to --link soft to be run in Tower #219

Open projassanchez opened 6 months ago

projassanchez commented 6 months ago

Hi, fusioncatcher fails when it is run in Tower eg:

Traceback (most recent call last): File "/opt/fusioncatcher/v1.33/bin/remove-adapter.py", line 1272, in main() File "/opt/fusioncatcher/v1.33/bin/remove-adapter.py", line 1268, in main options.processes) File "/opt/fusioncatcher/v1.33/bin/remove-adapter.py", line 1079, in trim_adapter linkit(input_file_1,output_file_1,kind=link) File "/opt/fusioncatcher/v1.33/bin/remove-adapter.py", line 104, in linkit print >>sys.stderr,"WARNING: Cannot do hard links ('%s' and '%s')!" % (linkto,file_output) UnboundLocalError: local variable 'linkto' referenced before assignment

Could be possible to change the remove-adapter.py \ 1146 --processes 12 \ 1147 --input_1 //work/scratch/5HyTfJeqqZ8kAX/27/012aeab7afbbef5f1d4c0ca79e4b36/init-f-0_blox-0_1.fq \ 1148 --input_2 /work/scratch/5HyTfJeqqZ8kAX/27/012aeab7afbbef5f1d4c0ca79e4b36/init-r-1_blox-0_2.fq \ 1149 --output_1 /work/scratch/5HyTfJeqqZ8kAX/27/012aeab7afbbef5f1d4c0ca79e4b36/init-noadapt-0_blox-0_1.fq \ 1150 --output_2 /work/scratch/5HyTfJeqqZ8kAX/27/012aeab7afbbef5f1d4c0ca79e4b36/init-noadapt-1_blox-0_2.fq \ 1151 --trim-n 3 \ 1152 --link hard \ 1153 > /work/scratch/5HyTfJeqqZ8kAX/27/012aeab7afbbef5f1d4c0ca79e4b36/log_adapters_0.txt \

for --link soft ?