correct lp2300 script

script/runscript.sh

@@ -12,10 +12,14 @@
 #$ -e /home/mcariou/2021_legio/log/
 module load R
 
- 
-./4_parse_PSIblastTMP.sh  ~/2021_legio/out_blastn/lpg2300.psiblast  ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.1 0.1 1
 
+./4_parse_PSIblastTMP.sh  ~/2021_legio/out_blastn/lpg2300_prot.psiblast  ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_50_50 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.5 0.5 1
 
+./4_parse_PSIblastTMP.sh  ~/2021_legio/out_blastn/lpg2300_prot.psiblast  ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_30_50 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.3 0.5 1
+
+./4_parse_PSIblastTMP.sh  ~/2021_legio/out_blastn/lpg2300_prot.psiblast  ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_50_30 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.5 0.3 1
+
+./4_parse_PSIblastTMP.sh  ~/2021_legio/out_blastn/lpg2300_prot.psiblast  ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_30_30 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.3 0.3 1
 
 
 

script/runscript_78Lp_step34.sh

+#!/bin/bash
+#$ -S /bin/bash
+## name of the job to follow them
+#$ -N runscript34
+## name of the queue to be used
+#$ -q E5-2670deb*,E5-2667v2*,E5-2667v4*
+#$ -cwd
+#$ -V
+## where to put the log files (output and error) automatically generated by the cluster (different from the .log generated by DGINN)
+## the dirs must exist before job is launched
+#$ -o /home/mcariou/2021_legio/log/
+#$ -e /home/mcariou/2021_legio/log/
+
+
+/home/mcariou/2021_legio/phylolegio/script/3_make_PSIblast.sh ~/2021_legio/blastdb/phyloref/phyloref_prot ~/2021_legio/genes/78Lp_uniprot.fasta ~/2021_legio/out_blastn/
+
+
+## Doesn't accomodate multi query yet
+#/home/mcariou/2021_legio/phylolegio/script/4_parse_PSIblastTMP.sh  ~/2021_legio/out_blastn/78Lp_uniprot.psiblast  ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_50_50 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.5 0.5 1
+
+
+# fin

script/runscript_lp2300_step3.sh

+#!/bin/bash
+#$ -S /bin/bash
+## name of the job to follow them
+#$ -N runscript3
+## name of the queue to be used
+#$ -q E5-2670deb*,E5-2667v2*,E5-2667v4*
+#$ -cwd
+#$ -V
+## where to put the log files (output and error) automatically generated by the cluster (different from the .log generated by DGINN)
+## the dirs must exist before job is launched
+#$ -o /home/mcariou/2021_legio/log/
+#$ -e /home/mcariou/2021_legio/log/
+
+
+/home/mcariou/2021_legio/phylolegio/script/3_make_PSIblast.sh ~/2021_legio/blastdb/phyloref/phyloref_prot ~/2021_legio/genes/lpg2300_prot.fasta ~/2021_legio/out_blastn/
+
+
+
+
+# fin

script/runscript_lp2300_step4.sh

+#!/bin/bash
+#$ -S /bin/bash
+## name of the job to follow them
+#$ -N runscript4
+## name of the queue to be used
+#$ -q E5-2670deb*,E5-2667v2*,E5-2667v4*
+#$ -cwd
+#$ -V
+## where to put the log files (output and error) automatically generated by the cluster (different from the .log generated by DGINN)
+## the dirs must exist before job is launched
+#$ -o /home/mcariou/2021_legio/log/
+#$ -e /home/mcariou/2021_legio/log/
+module load R
+
+
+./4_parse_PSIblastTMP.sh  ~/2021_legio/out_blastn/lpg2300_prot.psiblast  ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_50_50 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.5 0.5 1
+
+./4_parse_PSIblastTMP.sh  ~/2021_legio/out_blastn/lpg2300_prot.psiblast  ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_30_50 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.3 0.5 1
+
+./4_parse_PSIblastTMP.sh  ~/2021_legio/out_blastn/lpg2300_prot.psiblast  ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_50_30 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.5 0.3 1
+
+./4_parse_PSIblastTMP.sh  ~/2021_legio/out_blastn/lpg2300_prot.psiblast  ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_30_30 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.3 0.3 1
+
+
+
+# fin