diff --git a/constants.py b/constants.py index 85baab7..35f939a 100644 --- a/constants.py +++ b/constants.py @@ -6,20 +6,15 @@ # on your computer. # # FragGeneScan -#FragGeneScan = '/u/zhiqxie/informatics/inst/FragGeneScan1.19/run_FragGeneScan.pl' -FragGeneScan = '/u/zhiqxie/informatics/inst/FragGeneScan1.30/run_FragGeneScan.pl' +FragGeneScan = '/apps/inst/FragGeneScan1.30/run_FragGeneScan.pl' # Hmmer -phmmer = '/u/zhiqxie/informatics/inst/hmmer-3.1b2/bin/phmmer' -hmmsearch = '/u/zhiqxie/informatics/inst/hmmer-3.1b2/bin/hmmsearch' +phmmer = '/apps/inst/hmmer-3.3/bin/phmmer' +hmmsearch = '/apps/inst/hmmer-3.3/bin/hmmsearch' # Blast -blastn = '/l/ncbi-blast/bin/blastn' -blastp = '/l/ncbi-blast/bin/blastp' -makeblastdb = '/l/ncbi-blast/bin/makeblastdb' - -# get path where isescan.py is -import sys -path2isescan = os.path.dirname(sys.argv[0]) - +blastn = '/apps/inst/ncbi-blast-2.10.0+/bin/blastn' +blastp = '/apps/inst/ncbi-blast-2.10.0+/bin/blastp' +makeblastdb = '/apps/inst/ncbi-blast-2.10.0+/bin/makeblastdb' +# # Set the path variables pointing to the profile HMM files (clusters.single.faa and clusters.faa.hmm). # # The peptide sequences of single-member clusters, which is used by phmmer in hmmer