pinning python version for each environment, modifying TEMP install t…

…o ensure correct perl install is used

env_install.sh

@@ -11,7 +11,7 @@ conda remove -y -n MCCLINTOCK_popoolationte --all
 conda remove -y -n MCCLINTOCK_retroseq --all
 
 # create specific conda envs for McC main pipeilne
-conda create -y -n MCCLINTOCK_main
+conda create -y -n MCCLINTOCK_main python=3.6
 conda install -n MCCLINTOCK_main -y repeatmasker=4.0.7
 conda install -n MCCLINTOCK_main -y perl-bioperl-run=1.006900
 conda install -n MCCLINTOCK_main -y bwa=0.7.4
@@ -21,7 +21,7 @@ conda install -n MCCLINTOCK_main -y fastqc=0.11.2
 conda install -n MCCLINTOCK_main -y ucsc-fatotwobit=366
 
 # create specific conda envs for coverage module
-conda create -y -n MCCLINTOCK_cov
+conda create -y -n MCCLINTOCK_cov python=3.6
 conda install -n MCCLINTOCK_cov -y repeatmasker=4.0.7
 conda install -n MCCLINTOCK_cov -y perl-bioperl-run=1.006900
 conda install -n MCCLINTOCK_cov -y bwa=0.7.4
@@ -37,13 +37,13 @@ ln -s $lib_dir/libcrypto.so.1.1 $lib_dir/libcrypto.so.1.0.0
 source deactivate
 
 # create specific conda envs for ngs_te_mapper
-conda create -y -n MCCLINTOCK_ngstemapper
+conda create -y -n MCCLINTOCK_ngstemapper python=3.6
 conda install -n MCCLINTOCK_ngstemapper -y bwa=0.7.4
 conda install -n MCCLINTOCK_ngstemapper -y bedtools=2.17.0
 conda install -n MCCLINTOCK_ngstemapper -y r=3.5.0
 
 # create specific conda envs for temp
-conda create -y -n MCCLINTOCK_temp
+conda create -y -n MCCLINTOCK_temp python=3.6
 conda install -n MCCLINTOCK_temp -y perl-bioperl-run=1.006900
 conda install -n MCCLINTOCK_temp -y bwa=0.7.4
 conda install -n MCCLINTOCK_temp -y bedtools=2.17.0
@@ -52,32 +52,32 @@ conda install -n MCCLINTOCK_temp -y ucsc-fatotwobit=366
 conda install -n MCCLINTOCK_temp -y ucsc-twobittofa=366
 
 # create specific conda envs for relocate
-conda create -y -n MCCLINTOCK_relocate
+conda create -y -n MCCLINTOCK_relocate python=3.6
 conda install -n MCCLINTOCK_relocate -y perl-bioperl-run=1.006900
 conda install -n MCCLINTOCK_relocate -y bedtools=2.17.0
 conda install -n MCCLINTOCK_relocate -y bowtie=1.0.0
 conda install -n MCCLINTOCK_relocate -y ucsc-blat=366
 conda install -n MCCLINTOCK_relocate -y samtools=0.1.19
 
 # create specific conda envs for telocate
-conda create -y -n MCCLINTOCK_telocate
+conda create -y -n MCCLINTOCK_telocate python=3.6
 conda install -n MCCLINTOCK_telocate -y perl-bioperl-run=1.006900
 conda install -n MCCLINTOCK_telocate -y bwa=0.7.4
 conda install -n MCCLINTOCK_telocate -y bedtools=2.17.0
 conda install -n MCCLINTOCK_telocate -y java-jdk
 
 # create specific conda envs for MCCLINTOCK_populationte
-conda create -y -n MCCLINTOCK_popoolationte
+conda create -y -n MCCLINTOCK_popoolationte python=3.6
 conda install -n MCCLINTOCK_popoolationte -y perl-bioperl-run=1.006900
 conda install -n MCCLINTOCK_popoolationte -y bwa=0.7.4
 conda install -n MCCLINTOCK_popoolationte -y bedtools=2.17.0
 conda install -n MCCLINTOCK_popoolationte -y samtools=0.1.19
 
 # create specific conda envs for MCCLINTOCK_retroseq
-conda create -y -n MCCLINTOCK_retroseq
+conda create -y -n MCCLINTOCK_retroseq python=3.6
 conda install -n MCCLINTOCK_retroseq -y perl-bioperl-run=1.006900
 conda install -n MCCLINTOCK_retroseq -y bwa=0.7.4
 conda install -n MCCLINTOCK_retroseq -y bedtools=2.17.0
 conda install -n MCCLINTOCK_retroseq -y samtools=0.1.19
 conda install -n MCCLINTOCK_retroseq -y bcftools=1.2
-conda install -n MCCLINTOCK_retroseq -y exonerate=2.4.0
+conda install -n MCCLINTOCK_retroseq -y exonerate=2.4.0

install.sh

@@ -68,6 +68,12 @@ perlPath=$(which perl | sed 's/\//\\\//g')
 sed -i 's/\/usr\/bin\/perl -w/'"$perlPath"'/' RelocaTE/scripts/*.pl
 source deactivate
 
+source activate MCCLINTOCK_temp
+perlPath=$(which perl | sed 's/\//\\\//g')
+sed -i 's/perl /'"$perlPath"' /g' TEMP/scripts/TEMP_Absence.sh
+sed -i 's/perl /'"$perlPath"' /g' TEMP/scripts/TEMP_Insertion.sh
+source deactivate
+
 # Remove deprecated use of defined from RelocaTE to reduce errors
 for f in RelocaTE/scripts/*.pl
 do
@@ -178,4 +184,4 @@ echo "Testing dependencies for McClintock RetroSeq module..."
 dependencies_retroseq=("perl" "bedtools" "bwa" "samtools" "bcftools" "exonerate")
 source activate MCCLINTOCK_retroseq
 check_dependency "${dependencies_retroseq[@]}"
-source deactivate
+source deactivate