Remove further instances of writing to /dev/stderr

aux/sh/irap_fun.sh

@@ -172,7 +172,7 @@ function get_param_value {
 function get_cached_value {
 
     if [ ! -e $name/cached_vars.mk ]; then
-	echo ERROR: File $name/cached_vars.mk not found > /dev/stderr
+	echo ERROR: File $name/cached_vars.mk not found  1>&2
 	exit 1
     fi
     val=`grep "^$1=" $name/cached_vars.mk|cut -f 2 -d=`
@@ -489,10 +489,10 @@ function submit_jobs4target {
 }
 
 function get_pe_libs {
-    #echo $cmd conf=$conf $IRAP_PARAMS print_pe_libs se= > /dev/stderr
+    #echo $cmd conf=$conf $IRAP_PARAMS print_pe_libs se=  1>&2
     $cmd conf=$conf $IRAP_PARAMS print_pe_libs se= |tail -n 1
 }
 function get_se_libs {
-    #echo $cmd conf=$conf $IRAP_PARAMS print_se_libs pe= > /dev/stderr
+    #echo $cmd conf=$conf $IRAP_PARAMS print_se_libs pe=  1>&2
     $cmd conf=$conf $IRAP_PARAMS print_se_libs pe= | tail -n 1
 }

aux/sh/irap_shared.sh

@@ -107,12 +107,12 @@ function conf_get_species {
 function conf_ok {
     local conf=$1
     local irap_options=$2
-    echo  "irap conf=$conf $irap_options -n" > /dev/stderr
+    echo  "irap conf=$conf $irap_options -n"  1>&2
     set +e
     irap conf=$conf $irap_options -n 2>/dev/null    
     if [ $? == 2 ]; then
 	irap conf=$conf $irap_options -n
-	echo "ERROR: error in iRAP options." > /dev/stderr	
+	echo "ERROR: error in iRAP options."  1>&2	
 	exit 2
     fi
     set -e
@@ -125,15 +125,15 @@ function conf_get_var_value {
     local irap_options=$3
     # lookup in the conf file
     #
-    echo  "irap conf=$conf $irap_options -n | grep $conf_var=" > /dev/stderr
+    echo  "irap conf=$conf $irap_options -n | grep $conf_var="  1>&2
     d=`irap conf=$conf $irap_options pe= se= -n 2>/dev/null|grep -E "*\s*$conf_var\s*="|tail -n 1`
     if [ "$d-" == "-" ]; then
-	echo "ERROR: unable to get $conf_var value" > /dev/stderr	
+	echo "ERROR: unable to get $conf_var value"  1>&2	
 	exit 1
     else
 	d=`echo $d|cut -f 2 -d=`
     fi
-    echo "debug:$conf_var=$d" > /dev/stderr
+    echo "debug:$conf_var=$d"  1>&2
     echo $d
 }
 
@@ -235,7 +235,7 @@ function run_AND_timeIt {
     EXIT_STATUS=$?
     # output stderr
     #cat $sout >/dev/stdout
-    #cat $serr > /dev/stderr
+    #cat $serr  1>&2
 
     if [ $EXIT_STATUS -ne 0 ]; then
 	classify_error $label $serr
@@ -252,7 +252,7 @@ function run_AND_timeIt {
 function classify_error {
     perror "LOG files: $2"    
     ${1}_errors $2
-    #echo "!!!!!!!!!!!!!!$classified_error<<<<<<<<<<<<<<<<<<<<" > /dev/stderr
+    #echo "!!!!!!!!!!!!!!$classified_error<<<<<<<<<<<<<<<<<<<<"  1>&2
     print_classified_error
 }
 

aux/sh/lsf_shared_code.sh

@@ -72,15 +72,15 @@ function check_dependency {
 
 function stop_job {
     if [ "$DEBUG-" != "0-" ]; then
-	echo "stop/suspend job $1" > /dev/stderr
+	echo "stop/suspend job $1"  1>&2
     else
 	bstop -J $1
     fi
 }
 
 function resume_job {
     if [ "$DEBUG-" != "0-" ]; then
-	echo "resume job $1" > /dev/stderr
+	echo "resume job $1"  1>&2
     else
 	bresume -J $1
     fi
@@ -100,7 +100,7 @@ function submit_job_status {
     #p_info "WAITFOR (id)=$JOB_ID $jobname   $WAITFOR"
     # in spite of the checks, the job may have finished before launching the new one, hence catch the error and submit a new one if an error occurs
     if [ "$DEBUG-" == "2-" ]; then	
-	$ECHO $IRAP_PAR_CMD -n -q  > /dev/stderr
+	$ECHO $IRAP_PAR_CMD -n -q   1>&2
 	ret=$?
     else
 	$ECHO bsub $IRAP_LSF_PARAMS -M 1000 -R "select[mem>=1000]  rusage[mem=1000]" -q $QUEUE  -J "${jobname}n" $WAITFOR  irap_lsf_job_status.sh $jobname $JOB_ID  `get_maxmem $MEM` $LOG_DIR  $IRAP_PAR_CMD	

pcawg/irap_install_pcawg.sh

@@ -37,7 +37,7 @@ do
 done
 
 if [ "$DIR-" = "-" ]; then
-    echo "You need to provide the instalation directory" > /dev/stderr
+    echo "You need to provide the instalation directory"  1>&2
     exit 1
 fi
 

pcawg/irap_pcawg_align

@@ -10,7 +10,7 @@ DATA_TOPLEVEL_DIR=test_data
 metadata_file=$DATA_TOPLEVEL_DIR/metadata.tsv
 
 if [ "$id-" == "-" ]; then
-   echo "Usage: irap_pcawg_align  SOP tar.gz ID" > /dev/stderr
+   echo "Usage: irap_pcawg_align  SOP tar.gz ID"  1>&2
    exit 1
 fi
 
@@ -26,7 +26,7 @@ if [ "$tarball-" == "-" ]; then
 fi
 
 if [ ! -e $tarball ]; then
-   echo "$tarball not found" > /dev/stderr
+   echo "$tarball not found"  1>&2
    exit 1
 fi
 

pcawg/pcawg_sam_header.sh

@@ -7,30 +7,30 @@ meta_data_file=$3
 SOP_VERSION=1
 
 if [  "-$user_analysis_id" = "-" ]; then
-    echo "ERROR: analysis_id not given" > /dev/stderr
+    echo "ERROR: analysis_id not given"  1>&2
     exit 1
 fi
 if [  "-$file_prefix" = "-" ]; then
-    echo "ERROR: file_prefix not given" > /dev/stderr
+    echo "ERROR: file_prefix not given"  1>&2
     exit 1
 fi
 if [ ! -e "$meta_data_file" ]; then
-    echo "ERROR: $meta_data_file not found"  > /dev/stderr
+    echo "ERROR: $meta_data_file not found"   1>&2
    exit 1
 fi
 
 if [  "$file_prefix" == "icgc" ]; then                                            
      file_prefix=$user_analysis_id                                                 
 fi   
 if [ ! -e $meta_data_file ]; then
-    echo "ERROR: file $meta_data_file not found"  > /dev/stderr
+    echo "ERROR: file $meta_data_file not found"   1>&2
     exit 1
 fi
 
 # 
 sample_metadata=`grep -F "$file_prefix" $meta_data_file|tr '\t' '|'`
 if [ "-$sample_metadata" = "-" ]; then
-    echo "ERROR: Unable to find sample $file_prefix in $meta_data_file"  > /dev/stderr
+    echo "ERROR: Unable to find sample $file_prefix in $meta_data_file"   1>&2
     exit 1
 fi
 
@@ -60,13 +60,13 @@ done
 for var in analysis_id fastq_files center_name platform platform_model sample_id submitter_sample_id lib_id read_group_label fastq_files ; do
     #echo $var=${!var}
     if [ "${!var}-" == "-" ]; then
-	echo "ERROR: Unable to get value for $var"  > /dev/stderr
+	echo "ERROR: Unable to get value for $var"   1>&2
 	exit 1
     fi
 done
 # analysis id should match
 if [ "$analysis_id" != "$user_analysis_id" ]; then
-    echo "ERROR: Analysis id mismatch - expected $user_analysis_id and got $analysis_id"  > /dev/stderr
+    echo "ERROR: Analysis id mismatch - expected $user_analysis_id and got $analysis_id"   1>&2
     exit 1
 fi
 

scripts/atlas_clean_html.sh

@@ -1,12 +1,12 @@
 #!/usr/bin/env bash
 
 if [ "$1-" = "-" ] ; then
-    echo "atlas_clean_html.sh HTML file" > /dev/stderr
+    echo "atlas_clean_html.sh HTML file"  1>&2
     exit 1
 fi
 
 if [ ! -e "$1" ] ; then
-    echo "ERROR: file not found $1" > /dev/stderr
+    echo "ERROR: file not found $1"  1>&2
     exit 1
 fi
 

scripts/fastq_info.sh

@@ -3,14 +3,14 @@
 STDERR=/dev/stderr
 
 if [ "$*-" == "-"  ]; then
-    echo "fastq_info.sh .fastq [.fastq]" > $STDERR
+    echo "fastq_info.sh .fastq [.fastq]" >  1>&2
     exit 1
 fi
 
-A="`fastq_info $* 2>/dev/stdout | tee $STDERR |tail -n 5`"  
+A="`fastq_info $* 2>&1 | tee $STDERR |tail -n 5`"  
 ret=$?
 if [ $ret != 0 ]; then
-    echo "ERROR" > $STDERR
+    echo "ERROR" 1>&2
     exit $ret
 fi
 if [ `echo "$A"|grep -c -i "Error" ` != 0 ]; then
@@ -35,7 +35,7 @@ qual=`echo $A| sed -E "s/.*Quality encoding: ([0-9]+|solexa).*/\1/" `
 
 
 if [ "$qual-"  == "solexa-" ]; then
-    echo "ERROR: Quality encoding not supported by iRAP -  $qual" > /dev/stderr
+    echo "ERROR: Quality encoding not supported by iRAP -  $qual"  1>&2
     exit 1
 fi
 

scripts/fastq_validator.sh

@@ -18,7 +18,7 @@ if [ "$ext-" == "bam-" ]; then
     echo "Checking for unmapped reads"
     UN=`samtools view -c -f 4 $f`
     if [ "$UN-" == "0-" ]; then
-	echo "ERROR: No unaligned reads found in $f." > /dev/stderr
+	echo "ERROR: No unaligned reads found in $f."  1>&2
 	exit 1
     fi
     named_pipe=.`basename .$f`.pipe.fastq

scripts/fastqc2tsv

@@ -8,11 +8,11 @@ zip=y
 ifile=$1
 cat_cmd="unzip -p $ifile"
 if [ ! -e $ifile ] ; then
-   echo "$ifile not found" > /dev/stderr
+   echo "$ifile not found"  1>&2
    zip=n	
    ifile=`echo $ifile|sed "s/.fastqc.zip/_fastqc/"`
    if [ ! -e $ifile ] ; then 
-      echo "$ifile not found" > /dev/stderr	
+      echo "$ifile not found"  1>&2	
       exit 1
    fi   
    cat_cmd=cat		

scripts/irapBAM2stats.sh

@@ -3,12 +3,12 @@ set -e
 set -o pipefail
 
 if [ "$1-" = "-" ]; then
-    echo "Usage: irapBAM2stats2.sh bam_file_name" > /dev/stderr
+    echo "Usage: irapBAM2stats2.sh bam_file_name"  1>&2
     exit 1
 fi
 
 if [ ! -e $1.ridx ]; then
-    echo "Index not found: $1.ridx" > /dev/stderr
+    echo "Index not found: $1.ridx"  1>&2
     exit 1
 fi
 

scripts/irap_AE_setup.sh

@@ -48,7 +48,7 @@ function pinfo {
 }
 
 function perror {
-    echo "ERROR: $*" > /dev/stderr
+    echo "ERROR: $*"  1>&2
 }
 
 ## fix the filename by replacing some characters
@@ -343,7 +343,7 @@ if [ $skip_idf != "y" ]; then
 	irap_cmd=irap_sc
 	## expected number of clusters
 	if [ $(grep -c EAExpectedClusters $IDF_FILE_FP) -eq 0 ]; then
-	    echo ERROR: EAExpectedClusters not found in IDF > /dev/stderr
+	    echo ERROR: EAExpectedClusters not found in IDF  1>&2
 	    exit 1
 	fi
 	expected_clusters=$(grep EAExpectedClusters $IDF_FILE_FP|cut -f 2)
@@ -533,7 +533,7 @@ function download {
 	    set +e
 	    DOWNLOAD_PUBLIC $file $fn $download_program
 	    if [ $? -ne 0 ]; then
-	    echo "Failed to download from ENA  $file ..." > /dev/stderr
+	    echo "Failed to download from ENA  $file ..."  1>&2
 	    dl_fun="DOWNLOAD_PRIVATE"
 	fi
 	    set -e
@@ -544,11 +544,11 @@ function download {
 	    set +e
 	    DOWNLOAD_PRIVATE $file $fn $ID $SDRF_FILE_FP
 	    if [ $? -ne 0 ]; then
-		echo "Failed to download from private location $file ..." > /dev/stderr
+		echo "Failed to download from private location $file ..."  1>&2
 		stdbuf -o0 echo -n
 		DOWNLOAD_PRIVATE2 $file $fn $ID $SDRF_FILE_FP
 		if [ $? -ne 0 ]; then
-		    echo "Failed to download from private location2 $file ...given up" > /dev/stderr
+		    echo "Failed to download from private location2 $file ...given up"  1>&2
 		    exit 1
 		fi
 	    fi

scripts/irap_distrib_fastq.sh

@@ -6,12 +6,12 @@ data_dir=$3
 species=test_species
 
 if [ "$1-" == "-" ] ; then
-    echo "Usage: irap_distrib_fastq.sh irap_conf_file max_files_per_folder [data_dir]" > /dev/stderr
+    echo "Usage: irap_distrib_fastq.sh irap_conf_file max_files_per_folder [data_dir]"  1>&2
     exit 1
 fi
 
 if [ "$CONF-" == "-" ] || [ ! -e $CONF ]; then
-    echo "Unable to open configuration file" > /dev/stderr 
+    echo "Unable to open configuration file"  1>&2 
     exit 1
 fi
 if [ "$data_dir-" == "-" ]; then

scripts/irap_fastqc2tsv

@@ -13,16 +13,16 @@ zip=y
 ifile=$1
 cat_cmd="unzip -p $ifile"
 if [ ! -e $ifile ] ; then
-   echo "WARNING: $ifile not found" > /dev/stderr
+   echo "WARNING: $ifile not found"  1>&2
    zip=n	
    ifile=`echo $ifile|sed "s/.fastqc.zip/_fastqc/"`
    if [ ! -e $ifile ] ; then 
-       echo "ERROR: $ifile not found" > /dev/stderr	
+       echo "ERROR: $ifile not found"  1>&2	
       exit 1
    fi   
    cat_cmd=cat
 else
-    unzip -t $1 > /dev/stderr
+    unzip -t $1  1>&2
 fi
 pref=`basename $ifile|sed "s/.fastqc.zip//"|sed "s/_fastqc//"`
 echo "FASTQC $pref" | tr " " "\t"

scripts/irap_gen_version_mk.sh

@@ -8,15 +8,15 @@ echo  "# Generated `date` " > $DEST_FILE
 grep "VERSION=" $IRAP_DIR/scripts/irap_install.sh |sort -u | grep -v "^#"| sed -e "s/^ *//" >> $DEST_FILE
 # R packages
 if [ "`which R 2>/dev/null`-" = "-" ]; then
-    echo "R not found" > /dev/stderr
+    echo "R not found"  1>&2
 else
     irap_R_package_version.R edgeR Rsamtools limma baySeq limma DESeq2 piano DESeq DEXSeq SC3 Rtsne scater EBSeq baySeq Seurat  >> $DEST_FILE
 fi
 
 #if [ -x $IRAP_DIR/scripts/R3 ]; then
 #    irap_R3_package_version.R DESeq DEXSeq limma DESeq2 piano  >> $DEST_FILE
 #else 
-#    echo "R3 not found" > /dev/stderr
+#    echo "R3 not found"  1>&2
 #fi
 sed -i "s/VERSION=/version=/" $DEST_FILE
 exit 0

scripts/irap_install.sh

@@ -107,15 +107,15 @@ function download2cache {
     mkdir -p $SRC_DIR/download
     pushd $SRC_DIR/download
     PACKAGES2DOWNLOAD=`set  | grep _URL=|sed "s/_URL.*//"|grep -v "PACKAGES"|uniq`
-    echo $PACKAGES2DOWNLOAD > /dev/stderr
+    echo $PACKAGES2DOWNLOAD  1>&2
     for p in $PACKAGES2DOWNLOAD; do
 	URL=${p}_URL
 	FILE=${p}_FILE
 	pinfo "Downloading ($p)  ${!URL}"
 	download_software $p
 
 	if [ ! -e ${!FILE} ]; then
-	    echo "Failed downloading $p ${!URL}" > /dev/stderr
+	    echo "Failed downloading $p ${!URL}"  1>&2
 	    exit 1
 	else
 	    ls -lh ${!FILE}
@@ -2187,7 +2187,7 @@ fi
 
 
 if [ "$IRAP_DIR-" = "-" ]; then
-    echo ERROR: IRAP directory not defined. > /dev/stderr
+    echo ERROR: IRAP directory not defined.  1>&2
     usage
     exit 1    
 fi

scripts/irap_lsf_filter_logs.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 if [ "$1-" == "-" ]; then
-    echo "Usage: irap_lsf_filter_logs log_dir" > /dev/stderr
+    echo "Usage: irap_lsf_filter_logs log_dir"  1>&2
     exit 1
 fi
 
@@ -18,7 +18,7 @@ function check_jobs_status {
     out_files=`ls -1 $1/*.out 2>/dev/null`
     for f in $out_files; do
        OK=`grep -c -E  "^Successfully completed." $f`
-       #echo "OK=$OK" > /dev/stderr
+       #echo "OK=$OK"  1>&2
        if [ "$OK" == "1" ]; then
          let success_jobs=$success_jobs+1
        else