Mercurial > repos > davidvanzessen > shm_csr

comparison wrapper.sh @ 98:d714f5ea83d7 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
author rhpvorderman
date Wed, 10 Jan 2024 12:32:47 +0000
parents 385dea3c6cb5
children
comparison
equal deleted inserted replaced
97:fbc6307dd83b 98:d714f5ea83d7
20 naive_output_igm_naive_memory=${16} 20 naive_output_igm_naive_memory=${16}
21 filter_unique=${17} 21 filter_unique=${17}
22 filter_unique_count=${18} 22 filter_unique_count=${18}
23 class_filter=${19} 23 class_filter=${19}
24 empty_region_filter=${20} 24 empty_region_filter=${20}
25 fast=${21} 25 run_changeo=${21}
26 run_baseline=${22}
26 BASENAME=$(basename "$title") 27 BASENAME=$(basename "$title")
27 # Cut off .txz or .tgz suffix and also replace spaces with underscores. 28 # Cut off .txz or .tgz suffix and also replace spaces with underscores.
28 NEW_IMGT_PREFIX="new_IMGT_${BASENAME%.*}" 29 NEW_IMGT_PREFIX="new_IMGT_${BASENAME%.*}"
29 NEW_IMGT_PREFIX=${NEW_IMGT_PREFIX// /_} 30 NEW_IMGT_PREFIX=${NEW_IMGT_PREFIX// /_}
30 31
408 # Use a pipe so wc -l does not display the filename 409 # Use a pipe so wc -l does not display the filename
409 wc -l < 1_Summary.txt 410 wc -l < 1_Summary.txt
410 rm 1_Summary.txt 411 rm 1_Summary.txt
411 } 412 }
412 413
413 if [[ "$fast" == "no" ]] ; then 414 if [[ "$run_baseline" == "yes" ]] ; then
414 415
415 416
416 417
417 echo "---------------- baseline ----------------" 418 echo "---------------- baseline ----------------"
418 echo "---------------- baseline ----------------<br />" >> $log 419 echo "---------------- baseline ----------------<br />" >> $log
522 echo "<br />" >> $output 523 echo "<br />" >> $output
523 cat $dir/shm_csr.htm >> $output 524 cat $dir/shm_csr.htm >> $output
524 525
525 echo "</div>" >> $output #CSR tab end 526 echo "</div>" >> $output #CSR tab end
526 527
527 if [[ "$fast" == "no" ]] ; then 528 if [[ "$run_changeo" == "yes" ]] ; then
528 529
529 echo "---------------- change-o MakeDB ----------------" 530 echo "---------------- change-o MakeDB ----------------"
530 531
531 mkdir -p $outdir/change_o 532 mkdir -p $outdir/change_o
532 533