removed .sh block from gitignore

.gitignore

@@ -18,7 +18,7 @@
 *.docx
 *.pdf
 *.RDataTmp
-*.sh
+
 .Rproj.user/
 data/
 #processed_data/

processed_data/gbm/var_selection_master.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+#SBATCH --account GlobalDrivers
+#SBATCH --job-name=var_select_master
+##SBATCH --mail-type=FAIL,END
+##SBATCH [email protected]
+#SBATCH --partition normal
+#SBATCH --mem-per-cpu=1gb
+#SBATCH --cpus-per-task=1
+#SBATCH --time=00:05:00
+##SBATCH --ntasks=
+
+
+
+# model setup
+nmodels=5 # number of models per script: 
+starts=(1 6 11 16 21 26 31 36 41 46 51 56 61 66 71 76 81 86 91 96)
+var_type='mdr'
+
+export nmodels
+export var_type
+
+
+for ((i=0; i<=19; i++)) do
+  this_start=${starts[${i}]}
+  export this_start
+  echo Submitting bash script with starting point $this_start
+  sbatch var_selection_sequential.sh
+done

processed_data/gbm/var_selection_sequential.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+#SBATCH --account GlobalDrivers
+#SBATCH --job-name=GBM
+##SBATCH --mail-type=FAIL,END
+##SBATCH [email protected]
+#SBATCH --partition normal
+#SBATCH --mem-per-cpu=4gb
+#SBATCH --cpus-per-task=1
+#SBATCH --time=00:20:00
+##SBATCH --ntasks=
+
+
+source ~/miniconda3/bin/activate R-env-4
+
+echo Running script $i with starting point ${this_start[${i}]}
+Rscript gbm.R $nmodels $this_start $var_type > log_"$SLURM_JOB_ID"_"$this_start"_"$nmodels".txt

processed_data/sem/mod_selection_master.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+#SBATCH --account GlobalDrivers
+#SBATCH --job-name=mod_master
+##SBATCH --mail-type=FAIL,END
+##SBATCH [email protected]
+#SBATCH --partition normal
+#SBATCH --mem-per-cpu=1gb
+#SBATCH --cpus-per-task=1
+#SBATCH --time=00:05:00
+##SBATCH --ntasks=
+
+
+
+# setup for 32 jobs, runs in <1h
+nmodels=32704 # number of models per script: 31*32704 + 1*32705
+starts=(1 32705 65409 98113 130817 163521 196225 228929 261633 294337 327041 359745 392449 425153 457857 490561 523265 555969 588673 621377 654081 686785 719489 752193 784897 817601 850305 883009 915713 948417 981121 1013825)
+
+export nmodels
+
+
+for ((i=0; i<=31; i++)) do
+  this_start=${starts[${i}]}
+  export this_start
+  echo Submitting bash script with starting point $this_start
+  sbatch mod_selection_sequential.sh
+done

processed_data/sem/mod_selection_sequential.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+#SBATCH --account GlobalDrivers
+#SBATCH --job-name=SEM_Wednesdat_DivRate
+##SBATCH --mail-type=FAIL,END
+##SBATCH [email protected]
+#SBATCH --partition normal
+#SBATCH --mem-per-cpu=4gb
+#SBATCH --cpus-per-task=1
+#SBATCH --time=02:00:00
+##SBATCH --ntasks=
+
+
+source ~/miniconda3/bin/activate R-env-4
+
+echo Running script $i with starting point ${this_start[${i}]}
+Rscript 17_mod_selection_SEM_sequential_DivRate.R $nmodels $this_start > log_"$SLURM_JOB_ID"_"$this_start"_"$nmodels".txt

processed_data/sem/mod_selection_sequential_DivRate.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+#SBATCH --account GlobalDrivers
+#SBATCH --job-name=SEM_DivRate
+##SBATCH --mail-type=FAIL,END
+##SBATCH [email protected]
+#SBATCH --partition normal
+#SBATCH --mem-per-cpu=4gb
+#SBATCH --cpus-per-task=1
+#SBATCH --time=02:00:00
+##SBATCH --ntasks=
+
+
+source ~/miniconda3/bin/activate R-env-4
+
+echo Running script $i with starting point ${this_start[${i}]}
+Rscript 17_mod_selection_SEM_sequential_DivRate.R $nmodels $this_start > log_DivRate_"$SLURM_JOB_ID"_"$this_start"_"$nmodels".txt

processed_data/tact/tact_job_array.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+# submit_array.sh
+
+#SBATCH --account GlobalDrivers
+#SBATCH --job-name=GD_TACT
+#SBATCH --mail-type=FAIL,END
+#SBATCH [email protected]
+#SBATCH --partition normal
+#SBATCH --mem-per-cpu=145gb
+#SBATCH --cpus-per-task 1
+#SBATCH --time 90:00:00
+#SBATCH --array=400-450
+
+
+singularity exec tact.sif tact_build_taxonomic_tree goodsp.csv --output goodsp.taxonomy.tre &&
+
+source ~/miniconda3/bin/activate tact
+
+echo -e "\nrunning TACT\n"
+
+
+singularity exec tact.sif  tact_add_taxa --backbone gbmb_matched_no_misplaced.tre --taxonomy goodsp.taxonomy.tre --output gbmb_matched_no_misplaced_$SLURM_JOB_ID-$SLURM_ARRAY_TASK_ID.tacted --verbose