Commit b6ec5c5d authored by kbattenb's avatar kbattenb
Browse files

Removed my Japanese name from README.md.

parent 32c7a4b7

.gitlab-ci.yml

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# This file is a template, and might need editing before it works on your project.

# see https://docs.gitlab.com/ce/ci/yaml/README.html for all available options



# you can delete this line if you're not using Docker

image: busybox:latest



before_script:

  - echo "Installing cellranger dependencies"

  - apt-get install go rust rustup node python

  - export GOPATH="${HOME}/.go"

  - export GOROOT="$(brew --prefix golang)/libexec"

  - export PATH="$PATH:${GOPATH}/bin:${GOROOT}/bin"

  - test -d "${GOPATH}" || mkdir "${GOPATH}"

  - test -d "${GOPATH}/src/github.com" || mkdir -p "${GOPATH}/src/github.com"

  - export PATH=/usr/lib/go-1.11/bin:$PATH # Add golang to path

  - rustup install 1.28.0

  - rustup default 1.28.0

  - apt-get install make clang-6.0 golang-1.11-go libz-dev libbz2-dev liblzma-dev

  - echo "Creating cellranger test install"

  - git clone https://github.com/10XGenomics/cellranger.git

  - cd cellranger

  - git checkout 3.0.2

  - make

  - cd ..



#  - mkdir -p ~/local/bin

#  - if [[ -w ~/local/bin ]]; then echo "install directory writeable"; else echo "install directory not writeable"; fi

#  - cd ~/local/bin

#  - echo "Downloading cellranger"

#  - wget -O cellranger-3.1.0.tar.gz "http://cf.10xgenomics.com/releases/cell-exp/cellranger-3.1.0.tar.gz?Expires=1564080778&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cDovL2NmLjEweGdlbm9taWNzLmNvbS9yZWxlYXNlcy9jZWxsLWV4cC9jZWxscmFuZ2VyLTMuMS4wLnRhci5neiIsIkNvbmRpdGlvbiI6eyJEYXRlTGVzc1RoYW4iOnsiQVdTOkVwb2NoVGltZSI6MTU2NDA4MDc3OH19fV19&Signature=m6fJx3etqOoywnpHgADfRzpCSZ04YZEe0sA3ZyVl1EQMn5Zm60qLk7v4KVPRLy6a9Qi2zE5DKWr8EpFfAg3kWqZ5-vDYtZtlYAnl0~OhtijIyYs7Rm8Uqzal-lk8tmD4SQaZQVQY~RLEed7iWq7stYwc4QTXRUjtojGqwMvqf5t4dMQbn7tNs513shjC4lGfL7~xCWpc5vaxaSN9wGSRF8ex9Hy-GsMYG2Dm8ya7ajplR1SPqTcHd9sDfro1UzOK~IGkHh9GGO9EicXQ6ypExvKB-WrDLLLZ66rEJjeNoSS6qnTKeEzyKw-3UoEYfho~Ph4eKrFS-XSZhtEX-UDItg__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA"

#  - tar -xzvf cellranger-3.1.0.tar.gz

#  - echo "Downloading reference for human genome"

#  - wget http://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-GRCh38-3.0.0.tar.gz

#  - tar -xzvf refdata-cellranger-GRCh38-3.0.0.tar.gz

  - echo "cellranger added to PATH"

  - export PATH=./cellranger:$PATH

  - cellranger --version

  - cellranger testrun --id "test"

  - cd -

  

after_script:

  - echo "Testing complete"

   

build1:

  stage: build

  script:

    - echo "testing script call"

    - bash convert.sh --version

    - bash convert.sh --help

    - echo "testing setup"

    - bash convert.sh --technology "Nadia" --setup

    - bash convert.sh --technology "10x" --setup

    - bash convert.sh --technology "iCELL8" --setup

    - echo "conversion script configured and able to write to barcodes"

   

test1:

  stage: test

  script: convert.sh

    - echo "test 10x"

    - bash convert.sh -t "10x" -r "~/home/local/bin/cellranger-3.1.0/cellranger-tiny-ref/3.0.0" \

    - --read1 "~/home/local/bin/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L001_R1_001.fastq.gz" \

    - --read2 "~/home/local/bin/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L001_R2_001.fastq.gz"

    - echo "test Nadia"

    - bash convert.sh -t "Nadia" -r "~/home/local/bin/cellranger-3.1.0/cellranger-tiny-ref/3.0.0" \

    - --read1 "~/home/local/bin/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L001_R1_001.fastq.gz" \

    - --read2 "~/home/local/bin/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L001_R2_001.fastq.gz"

    - echo "test iCELL8"

    - bash convert.sh -t "Nadia" -r "~/home/local/bin/cellranger-3.1.0/cellranger-tiny-ref/3.0.0" \

    - --read1 "~/home/local/bin/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L001_R1_001.fastq.gz" \

    - --read2 "~/home/local/bin/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L001_R2_001.fastq.gz"

   

test2:

  stage: test 

  script: convert.sh

    - echo "test file inputs"

    - bash convert.sh -t "icell8" -r "~/home/local/bin/cellranger-3.1.0/cellranger-tiny-ref/3.0.0" \

    - -- file "~/home/local/lib/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L001" 

    - echo "test multiple lanes"

    - bash convert.sh -t "Nadia" -r "~/home/local/bin/cellranger-3.1.0/cellranger-tiny-ref/3.0.0" \

    - --read1 "~/home/local/bin/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L001_R1_001.fastq.gz" \

    - --read1 "~/home/local/bin/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L002_R1_001.fastq.gz" \

    - "~/home/local/bin/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L001_R2_001.fastq.gz"\

    - "~/home/local/bin/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L002_R2_001.fastq.gz"

    - echo "test file inputs"

    - bash convert.sh -t "icell8" -r "~/home/local/bin/cellranger-3.1.0/cellranger-tiny-ref/3.0.0" \

    - --file "~/home/local/bin/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L001" \

    - "~/home/local/bin/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L002"



   

deploy1:

  stage: deploy

  script:

    - echo "Checks completed"

README.md

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@@ -53,5 +53,5 @@ The script will: 
Please note that this script alters the barcode whitelist. Known iCELL8 barcodes are supported but this is not possible with Nadia or DropSeq chemistry so 100% valid barcodes will be returned.



This is a work-in-progress and documentation with examples will be added in the future. The script is stable and functional.

Please send feedback, comments, or issues to Kai Battenberg/辻井 快 <[kai.battenberg@riken.jp](mailto:kai.battenberg@riken.jp)>

Please send feedback, comments, or issues to Kai Battenberg <[kai.battenberg@riken.jp](mailto:kai.battenberg@riken.jp)>

 or Tom Kelly <[tom.kelly@riken.jp](mailto:tom.kelly@riken.jp)>

make_10x_barcodes.sh

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#find barcodes directory of local cellranger install

#cd /home/tom/local/bin/cellranger-2.1.0/cellranger-cs/2.1.0/lib/python/cellranger/barcodes

#cd /home/tom/local/bin/cellranger-3.0.2/cellranger-cs/3.0.2/lib/python/cellranger/barcodes

DIR=`which /home/tom/local/bin/cellranger-2.1.0/cellranger`

VERSION=`cellranger count --version | head -n 2 | tail -n 1 | cut -d"(" -f2 | cut -d")" -f1`

cd ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes



echo "update barcodes in ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes \n for cellranger version $VERSION installed in $DIR"



#restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8)

if [ -f nadia_barcode.txt -o -f  iCELL8_barcode.txt ]

    then

    echo "restore 10x barcodes

    cp 737K-august-2016.txt.backup 737K-august-2016.txt

    fi



echo "whitelist converted for 10x compatibility with version 2 kit"



#create version 3 files if version 3 whitelist available

if [ -f 3M-february-2018.txt.gz ]

    then

    #restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8)

    if [ -f nadia_barcode.txt -o -f  iCELL8_barcode.txt ]

        then

        echo "restore 10x barcodes

        cp 3M-february-2018.txt.gz.backup 3M-february-2018.txt.gz

        fi

    echo "whitelist converted for 10x compatibility with version 3 kit"

fi

make_iCELL8_barcodes.sh

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#find barcodes directory of local cellranger install

#cd /home/tom/local/bin/cellranger-2.1.0/cellranger-cs/2.1.0/lib/python/cellranger/barcodes

#cd /home/tom/local/bin/cellranger-3.0.2/cellranger-cs/3.0.2/lib/python/cellranger/barcodes

DIR=`which /home/tom/local/bin/cellranger-2.1.0/cellranger`

VERSION=`cellranger count --version | head -n 2 | tail -n 1 | cut -d"(" -f2 | cut -d")" -f1`

cd ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes



echo "update barcodes in ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes \n for cellranger version $VERSION installed in $DIR"



#restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8)

if [ -f nadia_barcode.txt -o -f  iCELL8_barcode.txt ]

    then

    echo "restore 10x barcodes"

    cp 737K-august-2016.txt.backup 737K-august-2016.txt

    fi



#create a file with every possible barcode (permutation)

if [ ! -f iCELL8_barcode.txt ]

    then

    #copy known iCell8 barcodes from convert repo to cellranger install

    cp iCell8_barcode.txt iCell8_barcode_converted.txt

    #convert barcode whitelist to match converted barcodes

    sed -i 's/^/AAAAA/g' iCell8_barcodes_converted.txt

    echo "expected barcodes generated for iCELL8"

    fi



#save original barcode file (if doesn't already exist)

if [ ! -f  737K-august-2016.txt.backup ]

    then

    echo "backup of version 2 whitelist"

    cp 737K-august-2016.txt 737K-august-2016.txt.backup

    fi



#combine 10x and Nadia barcodes

cat iCELL8_barcode_converted.txt > 737K-august-2016.txt

echo "whitelist converted for iCELL8 compatibility with version 2 kit"



#create version 3 files if version 3 whitelist available

if [ -f 3M-february-2018.txt.gz ]

    then

    #restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8)

    if [ -f nadia_barcode.txt -o -f  iCELL8_barcode.txt ]

        then

    echo "restore 10x barcodes"

    cp 3M-february-2018.txt.gz.backup 3M-february-2018.txt.gz

        fi

    gunzip -k  3M-february-2018.txt.gz

    if [ ! -f  3M-february-2018.txt.backup.gz ]

        then

        echo "backup of version 3 whitelist"

        cp 3M-february-2018.txt 3M-february-2018.txt.backup

        gzip 3M-february-2018.txt.backup

        fi

    #combine 10x and iCELL8 barcodes

    gzip -k iCELL8_barcode.txt

    cat iCELL8_barcode_converted.txt  > 3M-february-2018.txt

    gzip -f 3M-february-2018.txt

    echo "whitelist converted for iCELL8 compatibility with version 3 kit"

    fi

make_nadia_barcodes.sh

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#find barcodes directory of local cellranger install

#cd /home/tom/local/bin/cellranger-2.1.0/cellranger-cs/2.1.0/lib/python/cellranger/barcodes

#cd /home/tom/local/bin/cellranger-3.0.2/cellranger-cs/3.0.2/lib/python/cellranger/barcodes

DIR=`which /home/tom/local/bin/cellranger-2.1.0/cellranger`

VERSION=`cellranger count --version | head -n 2 | tail -n 1 | cut -d"(" -f2 | cut -d")" -f1`

cd ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes



echo "update barcodes in ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes \n for cellranger version $VERSION installed in $DIR"



#restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8)

if [ -f nadia_barcode.txt -o -f  iCELL8_barcode.txt ]

    then

    echo "restore 10x barcodes"

    cp 737K-august-2016.txt.backup 737K-august-2016.txt

    fi



#create a file with every possible barcode (permutation)

if [ ! -f nadia_barcode.txt ]

    then

    echo AAAA{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G} | sed 's/ /\n/g' > nadia_barcode.txt

    echo "expected barcodes generated for Nadia"

    fi 



#save original barcode file (if doesn't already exist)

if [ ! -f  737K-august-2016.txt.backup ]

    then

    echo backup of version 2 whitelist

    cp 737K-august-2016.txt 737K-august-2016.txt.backup

    fi



#combine 10x and Nadia barcodes

cat nadia_barcode.txt 737K-august-2016.txt.backup > 737K-august-2016.txt

echo "whitelist converted for Nadia compatibility with version 2 kit"



#create version 3 files if version 3 whitelist available

if [ -f 3M-february-2018.txt.gz ]

    then

    #restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8)

    if [ -f nadia_barcode.txt -o -f  iCELL8_barcode.txt ]

        then

        echo "restore 10x barcodes"

        cp 3M-february-2018.txt.gz.backup 3M-february-2018.txt.gz

        fi

    gunzip -k  3M-february-2018.txt.gz

    if [ ! -f  3M-february-2018.txt.backup.gz ]

        then

        echo "backup of version 3 whitelist"

        cp 3M-february-2018.txt 3M-february-2018.txt.backup

        gzip 3M-february-2018.txt.backup

        fi

    #combine 10x and Nadia barcodes

    gzip -k nadia_barcode.txt

    zcat nadia_barcode.txt 3M-february-2018.txt.backup > 3M-february-2018.txt

    gzip -f 3M-february-2018.txt

    echo "whitelist converted for Nadia compatibility with version 3 kit"

fi

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