From b80feb6c3e7ed677c6be7111c12e5abcfcedbea8 Mon Sep 17 00:00:00 2001 From: Sebastian Bassi Date: Wed, 24 Jul 2024 15:02:56 -0700 Subject: [PATCH 1/3] Create Dockerfile --- Dockerfile | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 Dockerfile diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 000000000..1b03157e7 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,27 @@ +FROM python:3.10.14-slim-bullseye + +LABEL software="spades" \ + author="Sebastian Bassi " \ + base_image="python:3.10.14-slim-bullseye" \ + container="spades" \ + about.summary="genome assembler for single-cell and isolates data sets" \ + about.home="https://ablab.github.io/spades/" \ + software.version="4.0.0" \ + upstream.version="4.0.0" \ + version="1" \ + extra.identifiers.biotools="spades" \ + about.copyright="2011-2014 Saint-Petersburg Academic University" \ + about.license="GPL-2+" \ + about.license_file="/usr/share/doc/spades/copyright" \ + extra.binaries="/usr/bin/metaspades,/usr/bin/metaspades.py,/usr/bin/plasmidspades,/usr/bin/plasmidspades.py,/usr/bin/rnaspades,/usr/bin/rnaspades.py,/usr/bin/spades,/usr/bin/spades.py,/usr/bin/truspades,/usr/bin/truspades.py" \ + about.tags="biology::nucleic-acids, field::biology, field::biology:bioinformatics,:c++,:python, interface::commandline,:program, scope::utility, works-with::biological-sequence,:file" + +USER root + +RUN apt-get update && apt-get install -y build-essential cmake wget libbz2-dev + +RUN wget https://github.com/ablab/spades/releases/download/v4.0.0/SPAdes-4.0.0.tar.gz + +RUN tar xfz SPAdes-4.0.0.tar.gz && rm SPAdes-4.0.0.tar.gz && cd SPAdes-4.0.0/ && ./spades_compile.sh + +# ./SPAdes-4.0.0/bin/spades.py --test From 35e82ff81ab7056ebadbe5bb246ef2460b898591 Mon Sep 17 00:00:00 2001 From: Sebastian Bassi Date: Wed, 24 Jul 2024 16:19:48 -0700 Subject: [PATCH 2/3] Update Dockerfile --- Dockerfile | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/Dockerfile b/Dockerfile index 1b03157e7..d15fa4617 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,13 +7,9 @@ LABEL software="spades" \ about.summary="genome assembler for single-cell and isolates data sets" \ about.home="https://ablab.github.io/spades/" \ software.version="4.0.0" \ - upstream.version="4.0.0" \ - version="1" \ extra.identifiers.biotools="spades" \ - about.copyright="2011-2014 Saint-Petersburg Academic University" \ + about.paper="Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A (2020) Using SPAdes de novo assembler. Current Protocols in Bioinformatics 70(1): e102. https://doi.org/10.1002/cpbi.102" \ about.license="GPL-2+" \ - about.license_file="/usr/share/doc/spades/copyright" \ - extra.binaries="/usr/bin/metaspades,/usr/bin/metaspades.py,/usr/bin/plasmidspades,/usr/bin/plasmidspades.py,/usr/bin/rnaspades,/usr/bin/rnaspades.py,/usr/bin/spades,/usr/bin/spades.py,/usr/bin/truspades,/usr/bin/truspades.py" \ about.tags="biology::nucleic-acids, field::biology, field::biology:bioinformatics,:c++,:python, interface::commandline,:program, scope::utility, works-with::biological-sequence,:file" USER root From 2f994e8a4b3fda08cf9631c9a97170c564e22888 Mon Sep 17 00:00:00 2001 From: Sebastian Bassi Date: Thu, 25 Jul 2024 12:12:27 -0700 Subject: [PATCH 3/3] Update Dockerfile --- Dockerfile | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index d15fa4617..b14f27da8 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,10 +14,14 @@ LABEL software="spades" \ USER root -RUN apt-get update && apt-get install -y build-essential cmake wget libbz2-dev +RUN apt-get update && apt-get install -y build-essential cmake wget libbz2-dev git RUN wget https://github.com/ablab/spades/releases/download/v4.0.0/SPAdes-4.0.0.tar.gz -RUN tar xfz SPAdes-4.0.0.tar.gz && rm SPAdes-4.0.0.tar.gz && cd SPAdes-4.0.0/ && ./spades_compile.sh +RUN tar xfz SPAdes-4.0.0.tar.gz && rm SPAdes-4.0.0.tar.gz && cd SPAdes-4.0.0/ && \ + cmake -B build/ -S src/ -DSPADES_USE_NCBISDK=ON -DSPADES_ENABLE_PROJECTS=all && \ + cmake --build build/ && cmake --install build/ && cd .. && rm -rf SPAdes-4.0.0/ -# ./SPAdes-4.0.0/bin/spades.py --test +CMD ["/bin/bash"] + +# spades.py --test