29072024 update

Vini

@@ -88,10 +88,12 @@ then
         echo "export job_status=qstat" >> $vini_dir/globals
         echo "export job_submit=qsub"  >> $vini_dir/globals
         echo "export job_cancel=qdel"  >> $vini_dir/globals
-        echo "PBS partitions are configured as:" ; pbsnodes
+        echo "PBS partitions are configured as:" ; qstat -Q
 	read -p "Enter the name of PBS partition Vini will use:" partition
-        cores=$(pbsnodes -a | sed -n "/partition=$partition/,/Mom=/p" | sed -n 's/^ *resources_available.ncpus = \([0-9]*\)/\1/p' | head -n 1)
-        memsize=$(pbsnodes -a | sed -n "/partition=$partition/,/Mom=/p" | sed -n 's/^ *resources_available.mem = \([0-9]*\)kb/\1/p' | head -n 1)
+        #cores=$(pbsnodes -a | sed -n "/partition=$partition/,/Mom=/p" | sed -n 's/^ *resources_available.ncpus = \([0-9]*\)/\1/p' | head -n 1)
+        #memsize=$(pbsnodes -a | sed -n "/partition=$partition/,/Mom=/p" | sed -n 's/^ *resources_available.mem = \([0-9]*\)kb/\1/p' | head -n 1)
+        cores=48
+        memsize=256GB
         echo "export partition=${partition}" >> $vini_dir/globals
         echo "export cores=${cores}"         >> $vini_dir/globals
         echo "export memsize=${memsize}" >> $vini_dir/globals
@@ -110,6 +112,7 @@ else
     echo "export memsize=${memsize}" >> $vini_dir/globals
 fi
 
+
 echo -n "Cancelling any remaining jobs from the previous run, please wait..."
 
 $job_status -u $USER > jobs
@@ -182,10 +185,8 @@ sh $vini_dir/download_Drugbank_fasta_structures            #download fasta files
 
 echo "AlphaFold will be used for protein structures prediction."
 echo "AlphaFold is using 128 cores and 225 GB per node"
-partition=`cat active_partition`
 echo "export AlphaFold_base=full_dbs" >> $vini_dir/globals
 echo "export cpus=128" >> $vini_dir/globals
-echo "export partition=${active_partition}" >> $vini_dir/globals
 
 read -e -p "Include cancer gene expressions and mutations from COSMIC into analysis (y/n)? Press enter to accept the default: " -i "n" cosmic
 

create_NSC_numbers_file

@@ -1,4 +1,3 @@
-ONES=1
 
 source $vini_dir/sourceme
 
@@ -47,7 +46,6 @@ then
     echo -n "Downloading AgentInfo file..."
     curl -o tmp -Ls https://ctepcore.nci.nih.gov/webobjs/CTEPWebsite/AgentInfo.html 
     python $HOME/.local/bin/html2text tmp > AgentInfo
-    rm AgentInfo.htlm
     echo "done."
 fi
 

generate_sbatch_command.sh

@@ -1,20 +1,20 @@
 
 if [ "$#" -lt 8 ]; then # Check if the correct number of arguments is provided
-    echo "Usage: $0 <input_list> <input_list> <slurm_script> <output_command_file> <I> <J> <L> <M>"
+    echo "Usage: $0 <input_list> <input_list> <wlm_script> <output_command_file> <I> <J> <L> <M>"
     exit 1
 fi
 
 input_list=$1
 out_list=$2
-slurm_script=$3
+wlm_script=$3
 output_command_file=$4
 I=$5 ; J=$6 ; L=$7 ; M=$8
 
 echo $I $J $L $M
 
 if  [ ${input_list} == "NONE" ]
 then
-    sbatch_command="jobid=\$(sbatch $slurm_script)"
+    sbatch_command="jobid=\$(sbatch $wlm_script)"
 
 else                              # Read the input list and extract job IDs
     job_dependencies="" 
@@ -27,7 +27,7 @@ else                              # Read the input list and extract job IDs
             job_dependencies="$job_dependencies,$job_id"
         fi
     done < "$input_list"
-    sbatch_command="jobid=\$(sbatch --dependency=afterany:$job_dependencies $slurm_script)"
+    sbatch_command="jobid=\$(sbatch --dependency=afterany:$job_dependencies $wlm_script)"
 
 fi
 

genes/Uniprot_ID_list

@@ -1,98 +1,98 @@
-Q9GZP0
-P08254
-P38936
+P01127
+P24864
 P07288
-P24941
-P10398
-Q02930
-Q9NQB0
-Q14209
-Q04206
-P37275
-P11308
-O96020
-P31751
+P27361
 P01112
+Q9GZP0
+P09211
+P04049
+P00750
+P06400
+Q92569
+P42345
 P62993
-P27930
-P14616
-P31213
-P28482
+Q9HCS4
+Q70SY1
+P08069
+P46527
+P31749
+P36507
 O15393
-P04637
-Q92793
-Q8TEY5
+O00716
 P16234
-O00329
 P10275
+P42338
+Q01094
+P31751
+P21802
+P00749
+O15111
+Q99801
+P09619
 P60484
-P01111
-P42345
-O14920
-Q02750
-P18848
-Q92569
-Q96BA8
-P01135
+O43889
+Q68CY7
 P01133
-P36402
+P05019
+P16220
+P38936
+P10398
+Q68CJ9
+P35222
+O14920
+Q92793
+P27930
+Q14209
+P00533
+O15530
+Q07890
+Q09472
 Q12778
-P42338
-P25963
+P27986
+P04626
 Q92934
-O43889
-O15111
+Q96BA8
+Q07889
+P24941
+P01111
+O00459
+Q9NQB0
+P04637
+P14616
+P11308
+Q02750
+Q9NRA1
+O00329
 P04085
-P00749
-Q09472
-P24864
-P42336
+Q02930
+Q00987
+P01308
+P31213
+P25963
 P24385
-Q99801
-P31749
-P19838
-P27361
-P46527
-P49841
-Q68CY7
-O00459
-Q07890
-P08238
-P09211
-P21802
-P55211
-O00716
-P41161
-Q9Y6K9
-P05019
-P00750
-P04049
+P14625
 P15056
-P01308
-P09619
-Q00987
-P01127
-P07900
-P00533
-P36507
 P11362
-P01116
-P06400
-P08069
-P35222
-P16220
-Q9NRA1
-Q70SY1
-Q01094
+Q9Y6K9
+P49841
+P08254
+Q8TEY5
+P01135
+P36402
+Q04206
 O43278
 P10415
-P04626
+P01116
+P28482
+Q9Y243
+P37275
+P08238
+O96020
+P19838
 P14780
-P27986
+P42336
+P07900
+P18848
+P55211
 Q9UJU2
-O15530
-Q68CJ9
-Q07889
-Q9Y243
-Q9HCS4
-P14625
+P41161