fixed absolute paths are now properly provided to the generated scripts

metaclade2

 #!/usr/bin/env bash
 #
-#  This file is part of MetaCLADE.
-#
-#  MetaCLADE is free software: you can redistribute it and/or modify
+#  This file is part of MetaCLADE2.
+# 
+#  MetaCLADE2 is free software: you can redistribute it and/or modify
 #  it under the terms of the CeCILL 2.1 Licence
 #
-#  MetaCLADE is distributed in the hope that it will be useful,
+#  MetaCLADE2 is distributed in the hope that it will be useful,
 #  but WITHOUT ANY WARRANTY; without even the implied warranty of
 #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 #
 #  You should have received a copy of the Licence CeCILL 2.1 along
-#  with MetaCLADE. If not, see <https://cecill.info/>.
+#  with MetaCLADE2. If not, see <https://cecill.info/>.
 #
 
 CMD_DIR=$(cd "$(dirname "${BASH_SOURCE[0]}" )" && pwd)

scripts/mclade_create_jobs.py

@@ -28,13 +28,14 @@ class CladeController:
             self.cladeCfgParser.read_file(clade_def) # first, read default values (read_file function must be used for those)
         # load user parameters
         self.fasta_path = os.path.abspath(args.fasta_path)
+        eprint(f"[{script_name}] fasta_path: {self.fasta_path}")
         self.name = args.name
         self.use_dama = args.use_dama
         self.usr_domain_list = args.usr_domain_list
         self.usr_domain_file = args.usr_domain_file
         self.evalue_cutoff = args.evalue_cutoff
         self.evalue_cutconf = args.evalue_cutconf
-        self.working_dir = args.work_dir
+        self.working_dir = os.path.abspath(args.work_dir)
         self.temp_out_path = f'{self.working_dir}/temp'
         self.jobs_out_path = f'{self.working_dir}/jobs'
         self.results_out_path = f'{self.working_dir}/results'

scripts/search_hmm.py

@@ -118,7 +118,7 @@ def main():
                     outFile.write(f'{modid}\t{modbeg}\t{modend}\t{modlen}\t{seqid}\t{seqenv_beg}\t{seqenv_end}\t{seqlen}\t{evalue}\t{bitscore}\t{alnacc}\n')
 
     os.remove(f'{temp_dir}/{args[ACC_ID]}.domtblout')
-    runtime = time.time()-start.time
+    runtime = time.time()-start_time
     print(f'[{script_name}] runtime: {args[ACC_ID]} HMM {runtime:.2f}')
     return 0