Merge branch 'devel'

nunofonseca · Nov 26, 2020 · 9aed5a6 · 9aed5a6
2 parents f24a1da + 1734a0d
commit 9aed5a6
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Showing 3 changed files with 21 additions and 10 deletions.
diff --git a/scripts/msi b/scripts/msi
@@ -19,7 +19,7 @@
 #
 # =========================================================
 
-MSI_VERSION="0.3.1"
+MSI_VERSION="0.3.2"
 PATH2SCRIPT=$(dirname "${BASH_SOURCE[0]}" )
 ## load shell functions
 source $PATH2SCRIPT/msi_shared.sh
@@ -344,6 +344,9 @@ if [ "$CONF_FILE-" != "-" ]; then
  pinfo "Loading $CONF_FILE...done." 
 fi
 
+## update some variables
+mbk_db=$TAXONOMY_DATA_DIR
+
 ## Check and validate arguments
 if [ "$TL_DIR-" == "-" ]; then
  perror "no value given to parameter -i"
@@ -829,7 +832,7 @@ function process_fastq {
  if [ "${MD[PRIMER_SET]^^}-" == "NONE-" ] ||
  [ "${MD[PRIMER_SET]^^}-" == "-" ] ; then
  pinfo "No primers for $fq_file"
- sed -E "s/ /_/g;s/size=(.*)$/\1/;s/$/:adapter=none:/" $CENTROIDS1 > $CENTROIDS.tmp && mv $CENTROIDS.tmp $CENTROIDS
+ sed -E "s/ /_/g;s/size=(.*)$/\1/;s/^>(.*)$/>\1:adapter=none:/" $CENTROIDS1 > $CENTROIDS.tmp && mv $CENTROIDS.tmp $CENTROIDS
 
  else
  pinfo "Calling cutadapter"

diff --git a/scripts/msi_install.sh b/scripts/msi_install.sh
@@ -22,7 +22,7 @@
 PATH2SCRIPT=$(dirname "${BASH_SOURCE[0]}" )
 
 ## OS tools
-SYSTEM_DEPS="wget gunzip grep git perl /usr/bin/time bash java pip3 python3 Rscript R make cmake"
+SYSTEM_DEPS="wget gunzip grep git perl /usr/bin/time bash java pip3 python3 Rscript R make cmake EMBOSS"
 
 SYSTEM_PACKS="ncurses-devel libcurl-devel openssl-devel pandoc python3-devel"
 
@@ -38,7 +38,7 @@ cutadapt_VERSION=2.10
 isONclust_VERSION=0.0.6
 
 
-metabinkit_VERSION=0.2.1
+metabinkit_VERSION=0.2.2
 metabinkit_URL=https://github.com/envmetagen/metabinkit/archive/${metabinkit_VERSION}.tar.gz
 
 fastq_utils_VERSION=0.24.1
@@ -60,6 +60,8 @@ CD_HIT_URL=https://github.com/weizhongli/cdhit/releases/download/V$CD_HIT_VERSIO
 racon_VERSION=1.4.13
 racon_URL="https://github.com/lbcb-sci/racon/releases/download/$racon_VERSION/racon-v${racon_VERSION}.tar.gz"
 
+emboss_VERSION=6.6.0
+
 envir_name=test_msi_env
 ####################################################################
 ##
@@ -259,7 +261,7 @@ if (version\$major > 3 || (version\$major == 3 && version\$minor>5)) {
 message("_____________________________________________________")
 
 message("Installing packages")
-packages2install<-c("Matrix","data.table","devtools","shiny","plotly","DT","r2d3","tidyr","sunburstR","d3heatmap","gplots","rmarkdown","flexdashboard","d3Tree")
+packages2install<-c("Matrix","data.table","devtools","shiny","plotly","DT","r2d3","tidyr","sunburstR","d3heatmap","gplots","rmarkdown","flexdashboard","d3Tree","R.utils")
 
 for (p in packages2install ) {
  message("PACKAGE:",p,"\n")
@@ -322,7 +324,7 @@ function install_all {
 }
 
 function msi_to_docker {
- MSI_VERSION="0.3.1"
+ MSI_VERSION="0.3.2"
  set -e
  echo "Generating docker image with MSI...this may take a while"
  pushd $PATH2SCRIPT/..
@@ -406,7 +408,7 @@ set +u
 ## Python
 export PYTHONUSERBASE=\$MSI_DIR/python
 export PYTHONPATH=$MSI_DIR/:$PYTHONPATH
-## lib64/$python_dir/site-packages:\$MSI_DIR/lib/$python_dir/site-packages:\$MSI_DIR/lib64/$python3_dir/site-packages:\$MSI_DIR/lib/$python3_dir/site-packages:$PYTHONPATH
+## lib64/$python_dir/site-packages:\$MSI_DIR/lib64/:$PYTHONPATH
 ## R packages
 export R_LIBS=\$MSI_DIR/Rlibs:\$R_LIBS
 PATH=\$MSI_DIR/python/bin:\$PATH
@@ -440,6 +442,7 @@ if [ "$CONDA_ENVIR-" == "1-" ]; then
  conda install -n $envir_name -c bioconda -c conda-forge minimap2=$minimap2_VERSION -y
  conda install -n $envir_name -c bioconda -c conda-forge cd-hit=$cd_hit_VERSION -y
  conda install -n $envir_name -c bioconda -c conda-forge racon=$racon_VERSION -y
+ conda install -n $envir_name -c bioconda -c conda-forge emboss=$emboss_VERSION -y
  #1.4.13-he513fc3_0
  #conda install -n $envir_name -c bioconda -c conda-forge pilon=1.23 -y
  echo "type

diff --git a/scripts/msi_rename_columns.sh b/scripts/msi_rename_columns.sh
@@ -90,15 +90,20 @@ OLD_COLUMN_NUM=$(get_metadata_col_pos $METADATA_COLUMN_OLD)
 NEW_COLUMN_NUM=$(get_metadata_col_pos $METADATA_COLUMN_NEW)
 
 tmp=$(mktemp -p . .msi_rename_XXX)
-zcat $TSV_FILE| tail -n +2 | sort -k1,1 > $tmp.1
+LC_ALL=C zcat $TSV_FILE| tail -n +2 | sort -k1b,1 > $tmp.1
 
 ## header
 set +e
 zcat $TSV_FILE |head -n 1
 set -e
-awk -v c1="${OLD_COLUMN_NUM}" -v c2="${NEW_COLUMN_NUM}" 'BEGIN {FS="\t"; OFS="\t"} {print $c1,$c2 }' $METADATAFILE | tail -n +2 | sort -k1,1 > $tmp.2
-join -t$'\t' $tmp.2 $tmp.1 | cut -f 2-
+if [ "$EXPERIMENT_ID-" != "-" ]; then
+ LC_ALL=C grep -E "(\s|^)$EXPERIMENT_ID(\s|$)" $METADATAFILE| awk -v c1="${OLD_COLUMN_NUM}" -v c2="${NEW_COLUMN_NUM}" 'BEGIN {FS="\t"; OFS="\t"} {print $c1,$c2 }' | sort -k1b,1 > $tmp.2
+else
+ LC_ALL=C awk -v c1="${OLD_COLUMN_NUM}" -v c2="${NEW_COLUMN_NUM}" 'BEGIN {FS="\t"; OFS="\t"} {print $c1,$c2 }' $METADATAFILE | tail -n +2 | sort -k1b,1 > $tmp.2
+fi
+
 
+LC_ALL=C join -t$'\t' $tmp.2 $tmp.1 | cut -f 2-
 rm -f $tmp.2 $tmp.1 $tmp
 
 exit 0