01_preparations.snake

shell.prefix("set -euo pipefail;")

rule all:
    """
    Right now the tarballs of trinity and trinotate
    """
    input:
        "src/trinityrnaseq-2.0.6/Trinity",
        "src/Trinotate-2.0.2/Trinotate",
        "src/TransDecoder-2.0.1/TransDecoder.LongOrfs",
        "data/db/uniprot_sprot.trinotate.pep",
        "data/db/uniprot_uniref90.trinotate.pep",
        "data/db/Pfam-A.hmm",
        "data/db/Trinotate.sqlite.gz"



rule clean:
    shell:
        """
        rm -rf src/trinityrnaseq-2.0.6
        rm -rf src/Trinotate-2.0.2
        rm -rf src/TransDecoder-2.0.1
        rm -rf data/db
        """



rule download_trinity:
    output:
        tarball = "src/trinityrnaseq-2.0.6.tar.gz"
    params:
        url = "https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.6.tar.gz"
    threads:
        1
    log:
        "src/trinityrnaseq-2.0.6.log"
    shell:
        """
        wget                        \
            -O  {output.tarball}    \
            {params.url}            \
        > {log} 2>&1
        """



rule install_trinity:
    input:
        tarball = "src/trinityrnaseq-2.0.6.tar.gz",
    output:
        script = "src/trinityrnaseq-2.0.6/Trinity",
    params:
        folder = "src/trinityrnaseq-2.0.6"
    threads:
        24
    shell:
        """
        tar xvf {input.tarball} -C src
        make -C {params.folder} -j {threads}
        touch {output.script}
        """



rule download_trinotate:
    output:
        tarball = "src/Trinotate-2.0.2.tar.gz"
    params:
        url = "https://github.com/Trinotate/Trinotate/archive/v2.0.2.tar.gz"
    threads:
        1
    log:
        "src/Trinotate-v2.0.2.log"
    shell:
        """
        wget                        \
            -O {output.tarball}     \
            {params.url}            \
        > {log} 2>&1
        """



rule install_trinotate:
    input:
        tarball = "src/Trinotate-2.0.2.tar.gz"
    output:
        script = "src/Trinotate-2.0.2/Trinotate"
    threads:
        1
    shell:
        """
        tar xvf {input.tarball} -C src
        touch {output.script}
        """



rule download_uniprot_sprot:
    output:
        "data/db/uniprot_sprot.trinotate.pep.gz"
    params:
        url= "ftp://ftp.broadinstitute.org/pub/Trinity/Trinotate_v2.0_RESOURCES/uniprot_sprot.trinotate_v2.0.pep.gz",
        folder= "data/db"
    threads:
        1
    shell:
        """
        mkdir -p {params.folder}
        wget {params.url} -O {output}
        """



rule makeblastdb_uniprot_sprot:
    input:
        "data/db/uniprot_sprot.trinotate.pep.gz"
    output:
        "data/db/uniprot_sprot.trinotate.pep"
    threads:
        1
    shell:
        """
        gzip -dc {input}        |
        makeblastdb             \
            -dbtype prot        \
            -title  {output}    \
            -out    {output}    \
        
        echo "This is a mock file for Snakemake" > {output}
        """



rule download_uniprot_uniref90:
    output:
        "data/db/uniprot_uniref90.trinotate.pep.gz"
    params:
        url= "ftp://ftp.broadinstitute.org/pub/Trinity/Trinotate_v2.0_RESOURCES/uniprot_uniref90.trinotate_v2.0.pep.gz",
        folder= "data/db"
    threads:
        1
    shell:
        """
        mkdir -p {params.folder}
        wget {params.url} -O {output}
        """



rule makeblatstdb_uniprot_uniref90:
    input:
        "data/db/uniprot_uniref90.trinotate.pep.gz"
    output:
        "data/db/uniprot_uniref90.trinotate.pep"
    threads:
        1
    shell:
        """
        gzip -dc {input}            |
        makeblastdb                 \
            -dbtype prot            \
            -title  {output}        \
            -out    {output}        \
        
        echo "This is a mock file for Snakemake" > {output}
        """



rule download_pfam_a:
    output:
        "data/db/Pfam-A.hmm.gz"
    params:
        url= "ftp://ftp.broadinstitute.org/pub/Trinity/Trinotate_v2.0_RESOURCES/Pfam-A.hmm.gz",
        folder= "data/db"
    threads:
        1
    shell:
        """
        mkdir -p {params.folder}
        wget {params.url} -O {output}
        """



rule hmmpress_pfam_a:
    input:
        "data/db/Pfam-A.hmm.gz"
    output:
        "data/db/Pfam-A.hmm"
    threads:
        1
    shell:
        """
        gunzip -k {input}
        hmmpress {output}
        printf "This is a mock file for Snakemake" > {output}
        """



rule download_sqlite_database:
    output:
        "data/db/Trinotate.sqlite.gz"
    params:
        url= "ftp://ftp.broadinstitute.org/pub/Trinity/Trinotate_v2.0_RESOURCES/Trinotate.sprot_uniref90.20150131.boilerplate.sqlite.gz",
        folder= "data/db"
    threads:
        1
    shell:
        """
        wget {params.url} -O {output}
        """



rule download_transdecoder:
    output:
        tarball= "src/TransDecoder-2.0.1.tar.gz"
    params:
        url= "https://github.com/TransDecoder/TransDecoder/archive/2.0.1.tar.gz",
    threads:
        1
    log:
        "src/TransDecoder-2.0.1.log"
    shell:
        """
        wget                    \
            -O {output.tarball} \
            {params.url}        \
        > {log} 2>&1
        """



rule install_transdecoder:
    input:
        tarball= "src/TransDecoder-2.0.1.tar.gz"
    output:
        script=  "src/TransDecoder-2.0.1/TransDecoder.LongOrfs"
    params:
        folder=  "src/TransDecoder-2.0.1/"
    threads:
        1
    shell:
        """
        tar tvf {input.tarball} -C src
        make -C {params.folder}
        touch {output.script}
        """