new salmon script and streaming diginorm out from Nov 2018

WhiteheadLab · Jul 28, 2019 · 66b79e2 · 66b79e2
1 parent 86ac14c
commit 66b79e2
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Showing 19 changed files with 915,745 additions and 3 deletions.
diff --git a/denovo_assembly_scripts/bridges/clusterfunc.py b/denovo_assembly_scripts/bridges/clusterfunc.py
@@ -80,7 +80,7 @@ def sbatch_file(basedir,process_name,module_name_list,filename,process_string):
         sbatch_file.write("#SBATCH -J "+process_name+"\n")
         sbatch_file.write("#SBATCH -o "+sbatch_dir+process_name+"-%j.o"+"\n")
         sbatch_file.write("#SBATCH -e "+sbatch_dir+process_name+"-%j.o"+"\n")
-        sbatch_file.write("#SBATCH -t 12:00:00"+"\n")
+        sbatch_file.write("#SBATCH -t 8:00:00"+"\n")
         #sbatch_file.write("#SBATCH -N 1"+"\n")
         sbatch_file.write("#SBATCH -p RM"+"\n")
         #sbatch_file.write("#SBATCH -p LM"+"\n")

diff --git a/denovo_assembly_scripts/bridges/salmon.py b/denovo_assembly_scripts/bridges/salmon.py
@@ -8,7 +8,7 @@
 def salmon_index(salmondir,assembly,genus_species):
     salmon_index_string="""
 #source /home/ljcohen/.bashrc
-#cd {}
+cd {}
 salmon index --index {} --transcripts {} --type quasi --threads 8
 """.format(salmondir,genus_species,assembly)
     print(salmon_index_string)
@@ -17,7 +17,7 @@ def salmon_index(salmondir,assembly,genus_species):
     module_name_list=""
     #s=subprocess.Popen(salmon_index_string,shell=True)
     #s.wait()
-    #clusterfunc.sbatch_file(salmondir,process_name,module_name_list,genus_species,commands)
+    clusterfunc.sbatch_file(salmondir,process_name,module_name_list,genus_species,commands)
     #return salmon_index_string
 
 def quant_salmon(salmondir,trimdir,genus_species,indexdir):

diff --git a/evaluation_data/diginorm_out/diginorm_stream-4524337.o b/evaluation_data/diginorm_out/diginorm_stream-4524337.o
diff --git a/evaluation_data/diginorm_out/diginorm_stream-4524338.o b/evaluation_data/diginorm_out/diginorm_stream-4524338.o
diff --git a/evaluation_data/diginorm_out/diginorm_stream-4524340.o b/evaluation_data/diginorm_out/diginorm_stream-4524340.o
diff --git a/evaluation_data/diginorm_out/diginorm_stream-4524341.o b/evaluation_data/diginorm_out/diginorm_stream-4524341.o
diff --git a/evaluation_data/diginorm_out/diginorm_stream-4524342.o b/evaluation_data/diginorm_out/diginorm_stream-4524342.o
diff --git a/evaluation_data/diginorm_out/diginorm_stream-4524343.o b/evaluation_data/diginorm_out/diginorm_stream-4524343.o
diff --git a/evaluation_data/diginorm_out/diginorm_stream-4524344.o b/evaluation_data/diginorm_out/diginorm_stream-4524344.o
diff --git a/evaluation_data/diginorm_out/diginorm_stream-4524345.o b/evaluation_data/diginorm_out/diginorm_stream-4524345.o
diff --git a/evaluation_data/diginorm_out/diginorm_stream-4524346.o b/evaluation_data/diginorm_out/diginorm_stream-4524346.o
diff --git a/evaluation_data/diginorm_out/diginorm_stream-4524347.o b/evaluation_data/diginorm_out/diginorm_stream-4524347.o
diff --git a/evaluation_data/diginorm_out/diginorm_stream-4524348.o b/evaluation_data/diginorm_out/diginorm_stream-4524348.o
diff --git a/evaluation_data/diginorm_out/diginorm_stream-4524349.o b/evaluation_data/diginorm_out/diginorm_stream-4524349.o