Commit 773f2ebc authored by kai.b's avatar kai.b
Browse files

adjusted to find SHELL

parent ba6cb1b8

launch_universc.sh

+92 −112
Original line number Diff line number Diff line
@@ -60,7 +60,7 @@ lastcall_u=`echo ${lastcall} | cut -f2 -d' '` 
lastcall_p=`echo ${lastcall} | cut -f3 -d' '`

barcodedir=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes #folder within cellranger with the whitelist barcodes

barcodefile=""

crIN=input4cellranger #name of the directory with all FASTQ files given to cellranger

crIN=input4cellranger #name of the directory with all FASTQ and index files given to cellranger

whitelistdir=${SDIR}/whitelists #path to whitelists

whitelistfile="outs/whitelist.txt" #name of the whitelist file added to the cellranger output

percellfile="outs/basic_stats.txt" #name of the file with the basic statistics of the run added to the cellranger output
@@ -91,44 +91,29 @@ fi 




#####usage statement#####

if [[ $VENDOR != "apple" ]]

    then

    SHELL=$(readlink -f /proc/$$/exe | cut -d'/' -f3)

else

    SHELL=$(ps -p $$ | awk '$1 == PP {print $4}' PP=$$)

fi

if [[ $(which launch_universc.sh) != *"not found" ]]

    then

    SHELL='' 

#get shell

invocation=$0

else

    if [[ -z $ZSH_VERSION ]]

        then

        SHELL="zsh"

    elif [[ -z $KSH_VERSION ]]

       then

       SHELL="ksh"

    elif [[ -z $FISH_VERSION ]]

       then

       SHELL="fish"

    elif [[ -z $BASH_VERSION ]]

        then

        SHELL="bash"

    else

       SHELL=$SHELL

    fi

    invocation=$(echo $(basename $0))

if [[ -n $BASH_VERSION ]]; then

    invocation='bash '${invocation}''

elif [[ -n $ZSH_VERSION ]]; then

    invocation='zsh '${invocation}''

elif [[ -n $FISH_VERSION ]]; then

    invocation='fish '${invoaction}''

elif [[ -n $KSH_VERSION ]]; then

    invocation='ksh '${invocation}''

fi



#usage statement

help='

Usage:

  '$SHELL' '$invocation' --testrun -t TECHNOLOGY

  '$SHELL' '$invocation' -t TECHNOLOGY --setup

  '$SHELL' '$invocation' -R1 FILE1 -R2 FILE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$SHELL' '$invocation' -R1 READ1_LANE1 READ1_LANE2 -R2 READ2_LANE1 READ2_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$SHELL' '$invocation' -f SAMPLE_LANE -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$SHELL' '$invocation' -f SAMPLE_LANE1 SAMPLE_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$SHELL' '$invocation' -v

  '$SHELL' '$invocation' -h

  '$invocation' --testrun -t TECHNOLOGY

  '$invocation' -t TECHNOLOGY --setup

  '$invocation' -R1 FILE1 -R2 FILE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$invocation' -R1 READ1_LANE1 READ1_LANE2 -R2 READ2_LANE1 READ2_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$invocation' -f SAMPLE_LANE -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$invocation' -f SAMPLE_LANE1 SAMPLE_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$invocation' -v

  '$invocation' -h



Convert sequencing data (FASTQ) from Nadia or ICELL8 platforms for compatibility with 10x Genomics and run cellranger count
@@ -301,7 +286,8 @@ for op in "$@"; do 
                echo "Error: file input missing for --index1"

                exit 1

            fi

            ;;        -f|--file)

            ;;        

        -f|--file)

            shift

            if [[ "$1" != "" ]]; then

                arg=$1
@@ -480,6 +466,8 @@ done 




#####check if this is a test run#####



#####################################

##  Note that tests are currently  ##

##        called the in the        ##

##       ./test directory          ##
@@ -505,7 +493,8 @@ if [[ $testrun == "true" ]]; then 
    if [[ $technology == "10x" ]]; then

        gunzip -fk ${SDIR}/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L00[12]_R[12]_001.fastq.gz

        read1=("${SDIR}/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_001.fastq" "${SDIR}/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R1_001.fastq")

        read2=("${SDIR}/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_002.fastq" "${SDIR}/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R2_001.fastq")

        read2=("${SDIR}/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R2_001.fastq" "${SDIR}/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R2_001.fastq")

        index1=("${SDIR}/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_I1_001.fastq.gz" "${SDIR}/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_I1_001.fastq.gz")

    elif [[ $technology == "nadia" ]]; then

        gunzip -fk ${SDIR}/test/shared/dropseq-test/SRR1873277_S1_L001_R[12]_001.fastq.gz

        read1=("${SDIR}/test/shared/dropseq-test/SRR1873277_S1_L001_R1_001.fastq")
@@ -769,86 +758,65 @@ fi 






#####Collecting R1 and R2 files#####

#####Check for presence of R1, R2, I1, and I2 files#####

#check for presence of read1 and read2 files

if [[ $verbose ]]; then

    echo " checking option: --read1 and --read2"

fi



#check for presence of read1 and read2 files

if [[ $setup == "false" ]]; then

    if [[ ${#read1[@]} -eq 0 ]]; then

        echo "Error: option -R1 or --file is required"

        echo "Error: option --read1 or --file is required"

        exit 1

    elif [[ ${#read2[@]} -eq 0 ]]; then

        echo "Error: option -R2 or --file is required"

        echo "Error: option --read2 or --file is required"

        exit 1

    fi

fi

keys=("R1" "R2")



# check if indexes given

#####check if indexes are given #####

#check for presence of indexe files

####################################

##   Note that indexes are not    ##

##    supported by conversion      ##

##    supported by launch_universc.sh     ##

##  You must demultiplex before   ##

##       calling cellranger       ##

##   This is a work-in-progress   ##

#####################################

if [[ ${#index1[@]} -eq ${#read1[@]} ]] || [[ ${#index1[@]} -ge 1 ]]; then

    if [[ ${#index1[@]} -eq 1 ]]; then

        echo " index1 $index1 passes"

    elif [[ ${#index1[@]} -ge 2 ]]; then

        echo " indices $index1 passes"

    else

        echo "WARNING: mismatch in number of files (check index I1 files)"

        echo "NOTE: if no index files are specified, these can be detected from R1 file names"

####################################

if [[ $verbose ]]; then

    echo " checking option: --index1 and --index2"

fi



#index 1

if [[ $setup == "false" ]]; then

    if [[ ${#index1[@]} -eq ${#read1[@]} ]]; then

        for i1 in "${index1[@]}"; do

            echo " index ${i1} passes"

        done

    else

    #if number of files mismatch or no index1 given

    echo " checking for index1 files..."

    for ii in $(seq 1 1 ${#read1[@]}); do

        #iterate over read1 inputs

        indexfile=${read1[$(( $ii -1 ))]}

        #derive I1 filename from R1 filename

        indexfile=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_I1/' )

        #only add index1 files to list variable if file exists

        if [[ -f $indexfile ]] || [[ -f ${indexfile}.gz ]] || [[ -f $indexfile.fastq ]] || [[ -f ${indexfile}.fastq.gz ]] || [[ -f $indexfile.fq ]] || [[ -f ${indexfile}.fq.gz ]]; then

            index1+=("$indexfile")

        #if no index1 is given

        if [[ ${#index1[@]} -eq 0 ]]; then

            echo " no index file was passed"

	else

            echo " one or more index1 files are missing"

	    echo " either give no index1 file, or give index1 file for each and every read1 file"

            exit 1

        fi

    fi

    done

fi



#check for dual indexing (I2 files)

#####check dual index(I1 and I2)#####

##  Note that indexes are copied   ##

##     but are not converted       ##

##   Demultiplex with bcl2fastq    ##

##   This is a work-in-progress    ##

#####################################

#index 2

if [[ $setup == "false" ]]; then

    #only check I2 for dual-indexed techniques

    if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sci-seq" ]] || [[ "$technology" == "smartseq" ]]; then

    if [[ ${#index2[@]} -eq ${#read1[@]} ]] || [[ ${#index2[@]} -ge 1 ]]; then

        if [[ ${#index2[@]} -eq 1 ]]; then

            echo " index2 $index2 passes"

        elif [[ ${#index2[@]} -ge 2 ]]; then

            echo " indices $index2 passes"

        if [[ ${#index2[@]} -eq ${#read1[@]} ]]; then        

            for i2 in "${index2[@]}"; do

                echo " index ${i2} passes"

	    done

        else

            echo "WARNING: mismatch in number of files (check index I2 files)"

            echo "NOTE: if no index files are specified, these can be detected from R1 file names"

            echo " one or more index2 files are missing"

            echo " either give no index files, or give index1 and index2 for each and every read1 and read2 file"

        fi

    else

        #if number of files mismatch or no index1 given

        echo " checking for index1 files..."

        for ii in $(seq 1 1 ${#read1[@]}); do

             #iterate over read1 inputs

             indexfile=${read1[$(( $ii -1 ))]}

             #derive I2 filename from R1 filename

             indexfile=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_I2/' )

             #only add index2 files to list variable if file exists

             if [[ -f $indexfile ]] || [[ -f ${indexfile}.gz ]] || [[ -f $indexfile.fastq ]] || [[ -f ${indexfile}.fastq.gz ]] || [[ -f $indexfile.fq ]] || [[ -f ${indexfile}.fq.gz ]]; then

                 index2+=("$indexfile")

             fi

        done

    fi   

fi
@@ -919,6 +887,18 @@ if [[ $verbose = "true" ]]; then 
    echo "${#index2[@]} I2s: ${index2[@]}"

fi























exit 0



#check number of index1 files is 0 or number of read1 files

if [[ ${#index1[@]} -eq ${#read1[@]} ]] || [[ ${#index1[@]} -eq 0 ]]; then

    if [[ ${#index1[@]} -eq ${#read1[@]} ]]; then

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