-
Notifications
You must be signed in to change notification settings - Fork 128
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* removed python * Update Dockerfile change license link --------- Co-authored-by: Kutluhan Incekara <[email protected]>
- Loading branch information
Showing
3 changed files
with
80 additions
and
1 deletion.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| FROM ubuntu:jammy AS app | ||
|
|
||
| # to make it easier to upgrade for new versions; ARG variables only persist during docker image build time | ||
| ARG SPADES_VER="4.1.0" | ||
|
|
||
| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="SPAdes" | ||
| LABEL software.version="${SPADES_VER}" | ||
| LABEL description="de novo DBG genome assembler" | ||
| LABEL website="https://github.com/ablab/spades" | ||
| LABEL license="https://github.com/ablab/spades/blob/main/LICENSE" | ||
| LABEL maintainer="Curtis Kapsak" | ||
| LABEL maintainer.email="[email protected]" | ||
|
|
||
| # install dependencies; cleanup apt garbage | ||
| # python v3.8.10 is installed here; point 'python' to python3 | ||
| RUN apt-get update && apt-get install --no-install-recommends -y \ | ||
| python3 \ | ||
| python3-distutils \ | ||
| wget \ | ||
| pigz \ | ||
| ca-certificates \ | ||
| libgomp1 && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* && \ | ||
| update-alternatives --install /usr/bin/python python /usr/bin/python3 10 | ||
|
|
||
| # install SPAdes binary; make /data | ||
| RUN wget -q https://github.com/ablab/spades/releases/download/v${SPADES_VER}/SPAdes-${SPADES_VER}-Linux.tar.gz && \ | ||
| tar -xzf SPAdes-${SPADES_VER}-Linux.tar.gz && \ | ||
| rm -r SPAdes-${SPADES_VER}-Linux.tar.gz && \ | ||
| mkdir /data | ||
|
|
||
| # set PATH and locale settings for singularity | ||
| ENV LC_ALL=C.UTF-8 \ | ||
| PATH="${PATH}:/SPAdes-${SPADES_VER}-Linux/bin" | ||
|
|
||
| CMD ["spades.py", "--help"] | ||
|
|
||
| WORKDIR /data | ||
|
|
||
| # test layer | ||
| FROM app AS test | ||
|
|
||
| # print version and run the supplied test flag | ||
| RUN spades.py --version && spades.py --help | ||
|
|
||
| # run the supplied test | ||
| RUN spades.py --test | ||
|
|
||
| WORKDIR /test | ||
|
|
||
| # run on some test files | ||
| RUN wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR323/020/SRR32343420/SRR32343420_1.fastq.gz && \ | ||
| wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR323/020/SRR32343420/SRR32343420_2.fastq.gz && \ | ||
| spades.py --isolate -1 SRR32343420_1.fastq.gz -2 SRR32343420_2.fastq.gz --threads 4 -o test && \ | ||
| head /test/test/contigs.fasta |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| # SPAdes | ||
|
|
||
| Main tool: [SPAdes](https://github.com/ablab/spades) | ||
|
|
||
| SPAdes genome assembler | ||
|
|
||
| ## Example commands | ||
|
|
||
| ```bash | ||
| # Test with supplied E. coli data | ||
| docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data staphb/spades:latest spades.py --test | ||
|
|
||
| # paired-end Illumina reads are in the $PWD | ||
| $ ls | ||
| SRR7062227_1.fastq.gz SRR7062227_2.fastq.gz | ||
|
|
||
| # assemble with your own data (broken into two lines for readability) | ||
| docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data staphb/spades:latest \ | ||
| spades.py -1 /data/SRR7062227_1.fastq.gz -2 /data/SRR7062227_2.fastq.gz -t 8 --isolate -o /data/SRR7062227-spades-output/ | ||
| ``` | ||
|
|
||
| View full `spades` help options: `docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data staphb/spades:latest spades.py --help` |