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.

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.

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)>
 
 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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