Merge branch 'dev'

README.md

@@ -97,7 +97,7 @@ This FROGS repository is for command line user. If you want to install FROGS on
 
 ## Tools dependancies
 
-FROGS is written in Python 3.7 (with external numpy and Scipy libraries) , uses also home-made scripts written in PERL5 and R 3.6.
+FROGS is written in Python 3 (with external numpy and Scipy libraries) , uses also home-made scripts written in PERL5 and R 4.
 
 FROGS relies on different specific tools for each of the analysis steps.
 

test/test_dependancies_frogsfunc.sh

@@ -2,7 +2,7 @@
 
 out_dir=res_4.0.0_to_check
 expected_dir=res_4.0.0_expected
-run_programs=false	## if true lance les python sinon, fait uniquement les comparatifs de résultats
+run_programs=false     ## if true lance les python sinon, fait uniquement les comparatifs de résultats
 
 ## Set ENV
 ## export PATH=../app:$PATH
@@ -35,15 +35,16 @@ echo "Step frogsfunc_placeseqs `date`"
 if $run_programs
 then
 	frogsfunc_placeseqs.py \
-	 --input-fasta $frogs_dir/test/data/frogsfunc.fasta \
-	 --input-biom $frogs_dir/test/data/frogsfunc.biom \
+	 --input-fasta data/frogsfunc.fasta \
+	 --input-biom data/frogsfunc.biom \
 	 --placement-tool sepp \
 	 --out-tree $out_dir/25-frogsfunc_placeseqs_tree.nwk \
 	 --excluded $out_dir/25-frogsfunc_placeseqs_excluded.txt \
 	 --insert-fasta $out_dir/25-frogsfunc_placeseqs.fasta \
 	 --insert-biom $out_dir/25-frogsfunc_placeseqs.biom \
 	 --closests-ref $out_dir/25-frogsfunc_placeseqs_closests_ref_sequences.txt \
-	 --html $out_dir/25-frogsfunc_placeseqs_summary.html 
+	 --html $out_dir/25-frogsfunc_placeseqs_summary.html \
+	 --log-file $out_dir/25-frogsfunc_placeseqs.log
 
 	if [ $? -ne 0 ]
 	then
@@ -91,8 +92,8 @@ then
 	 --tree $out_dir/25-frogsfunc_placeseqs_tree.nwk \
 	 --output-marker $out_dir/26-frogsfunc_copynumbers_marker.tsv \
 	 --output-function $out_dir/26-frogsfunc_copynumbers_predicted_functions.tsv \
-	 --html $out_dir/26-frogsfunc_copynumbers_summary.html
-
+	 --html $out_dir/26-frogsfunc_copynumbers_summary.html \
+	 --log-file $out_dir/26-frogsfunc_copynumbers.log
 	if [ $? -ne 0 ]
 	then
 	    echo "Error in frogsfunc_copynumbers " >&2
@@ -128,7 +129,8 @@ then
 	 --seqtab $out_dir/27-frogsfunc_functions_marker_norm.tsv \
 	 --weighted $out_dir/27-frogsfunc_functions_weighted_nsti.tsv \
 	 --excluded $out_dir/27-frogsfunc_functions_excluded.txt \
-	 --html $out_dir/27-frogsfunc_functions_excluded.txt
+	 --html $out_dir/27-frogsfunc_functions_excluded.txt \
+	 --log-file $out_dir/27-frogsfunc_functions.log
 
 	if [ $? -ne 0 ]
 	then
@@ -163,14 +165,15 @@ then
 fi
 
 
-echo "Step frogsfunc_placeseqs `date`"
+echo "Step frogsfunc_pathways `date`"
 
 if $run_programs
 then
 	frogsfunc_pathways.py \
 	 --input-file $out_dir/27-frogsfunc_functions_unstrat.tsv \
 	 --pathways-abund $out_dir/28-frogsfunc_pathways_unstrat.tsv \
-	 --html $out_dir/28-frogsfunc_pathways_summary.html
+	 --html $out_dir/28-frogsfunc_pathways_summary.html \
+	 --log-file $out_dir/28-frogsfunc_pathways.log
 
 	if [ $? -ne 0 ]
 	then
@@ -189,5 +192,4 @@ then
 	echo "Difference in frogsfunc_pathways : 28-rogsfunc_pathways_summary.html " >&2
 fi
 
-rm /tmp/tmp /tmp/tmp1
 echo "Completed with success"