Commit 7145874b authored by iquasere's avatar iquasere
Browse files

CI from Dockerfile

* won't work fom quay, since image only builds after release
parent 58eaad49
# This is a basic workflow to help you get started with Actions
name: CI
# Controls when the action will run.
on:
# Triggers the workflow on push or pull request events but only for the master branch
push:
branches: [ master ]
pull_request:
......@@ -23,13 +19,32 @@ jobs:
# Steps represent a sequence of tasks that will be executed as part of the job
steps:
# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
- uses: actions/checkout@v2
- name: Checkout
uses: actions/checkout@v2
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v1
# Runs a single command using the runners shell
- name: Get the docker image
run: docker run quay.io/biocontainers/mosca:1.3.5--0 /usr/local/share/MOSCA/scripts/mosca.py --version
- name: Build and push
uses: docker/build-push-action@v2
with:
context: .
file: ./Dockerfile
tags: mosca:latest
outputs: type=docker,dest=/tmp/mosca.tar
# Runs a set of commands using the runners shell
- name: Help command
run: |
docker run quay.io/biocontainers/mosca:1.3.5--0 /usr/local/share/MOSCA/scripts/mosca.py --help
use:
runs-on: ubuntu-latest
needs: build
steps:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v1
- name: Download artifact
uses: actions/download-artifact@v2
with:
name: mosca
path: /tmp
- name: Load Docker image
run: |
docker load --input /tmp/mosca.tar
docker image ls -a
......@@ -8,13 +8,16 @@ RUN buildDeps='build-essential zlib1g-dev' \
&& conda config --add channels bioconda \
&& conda config --add channels conda-forge \
&& git clone https://github.com/iquasere/MOSCA.git \
&& conda install svn reportlab openpyxl xlrd>=0.9.0 r-rcolorbrewer pandas scikit-learn lxml biopython perl \
&& conda install -c bioconda fastqc sortmerna=2.1 seqtk trimmomatic megahit spades fraggenescan diamond upimapi htseq bowtie2 maxbin2 checkm-genome bioconductor-deseq2=1.22.1 bioconductor-edger=3.24.3 r-pheatmap r-optparse blast krona seqkit samtools \
&& conda install -c conda-forge progressbar33 tqdm>=4.33.0 xlsxwriter unzip \
&& conda install -c bioconda -c conda-forge recognizer maxquant keggcharter quast \
# obtained with conda env export --no-builds > environment.yml
&& conda env create -f MOSCA/workflow/envs/environment.yml \
&& conda clean --all \
&& perl /opt/conda/opt/krona/install.pl \
&& svn export https://github.com/timflutre/trimmomatic/trunk/adapters MOSCA/Databases/illumina_adapters \
&& apt-get purge -y --auto-remove $buildDeps
&& apt-get purge -y --auto-remove $buildDeps \
&& dir="/share/MOSCA" \
&& mkdir -p "${dir}/scripts" "/bin" \
&& cp MOSCA/workflow/scripts/* "${dir}/scripts" \
&& cp MOSCA/workflow/Snakefile MOSCA/workflow/mosca.py "${dir}/scripts" \
&& cp -r resources "${dir}/resources" \
&& chmod +x "${dir}/scripts/mosca.py" \
&& ln -s "${dir}/scripts/mosca.py" "${PREFIX}/bin/"
ENTRYPOINT [ "python", "/MOSCA/scripts/mosca.py" ]
\ No newline at end of file
ENTRYPOINT [ "python", "${dir}/scripts/mosca.py" ]
\ No newline at end of file
name: mosca
channels:
- r
- conda-forge
- bioconda
- anaconda
- defaults
dependencies:
- _libgcc_mutex=0.1
- _openmp_mutex=4.5
- _r-mutex=1.0.1
- aioeasywebdav=2.4.0
- aiohttp=3.7.3
- alsa-lib=1.2.3
- amply=0.1.4
- appdirs=1.4.4
- apr=1.6.5
- async-timeout=3.0.1
- attmap=0.12.11
- attrs=20.3.0
- backports=1.0
- backports.functools_lru_cache=1.6.1
- bcrypt=3.2.0
- binutils_impl_linux-64=2.35.1
- binutils_linux-64=2.35
- bioconductor-affy=1.68.0
- bioconductor-affyio=1.60.0
- bioconductor-annotate=1.68.0
- bioconductor-annotationdbi=1.52.0
- bioconductor-biobase=2.50.0
- bioconductor-biocgenerics=0.36.0
- bioconductor-biocparallel=1.24.0
- bioconductor-delayedarray=0.16.0
- bioconductor-deseq2=1.30.0
- bioconductor-edger=3.32.0
- bioconductor-genefilter=1.72.0
- bioconductor-geneplotter=1.68.0
- bioconductor-genomeinfodb=1.26.0
- bioconductor-genomeinfodbdata=1.2.4
- bioconductor-genomicranges=1.42.0
- bioconductor-iranges=2.24.0
- bioconductor-limma=3.46.0
- bioconductor-matrixgenerics=1.2.0
- bioconductor-pcamethods=1.82.0
- bioconductor-preprocesscore=1.52.0
- bioconductor-rots=1.18.0
- bioconductor-s4vectors=0.28.0
- bioconductor-summarizedexperiment=1.20.0
- bioconductor-vsn=3.58.0
- bioconductor-xvector=0.30.0
- bioconductor-zlibbioc=1.36.0
- biopython=1.78
- blast=2.10.1
- boost-cpp=1.70.0
- boto3=1.16.28
- botocore=1.19.28
- bowtie2=2.3.5.1
- brotlipy=0.7.0
- bwidget=1.9.14
- bzip2=1.0.8
- c-ares=1.17.1
- ca-certificates=2020.12.5
- cachetools=4.1.1
- cairo=1.16.0
- certifi=2020.12.5
- cffi=1.14.4
- chardet=3.0.4
- checkm-genome=1.1.3
- circos=0.69.8
- coincbc=2.10.5
- configargparse=1.2.3
- cryptography=3.2.1
- curl=7.71.1
- cycler=0.10.0
- cyrus-sasl=2.1.27
- datrie=0.8.2
- decorator=4.4.2
- dendropy=4.5.1
- diamond=2.0.5
- docutils=0.16
- dropbox=10.9.0
- entrez-direct=13.9
- et_xmlfile=1.0.1
- expat=2.2.9
- fastqc=0.11.9
- fftw=3.3.8
- filechunkio=1.8
- font-ttf-dejavu-sans-mono=2.37
- font-ttf-inconsolata=2.001
- font-ttf-source-code-pro=2.030
- font-ttf-ubuntu=0.83
- fontconfig=2.13.1
- fonts-conda-forge=1
- fraggenescan=1.31
- freetype=2.10.4
- fribidi=1.0.10
- ftputil=4.0.0
- gcc_impl_linux-64=7.5.0
- gcc_linux-64=7.5.0
- gdk-pixbuf=2.42.0
- gettext=0.19.8.1
- gfortran_impl_linux-64=7.5.0
- gfortran_linux-64=7.5.0
- ghostscript=9.53.3
- giflib=5.2.1
- gitdb=4.0.5
- gitpython=3.1.11
- glib=2.66.3
- glimmerhmm=3.0.4
- google-api-core=1.23.0
- google-api-python-client=1.12.8
- google-auth=1.23.0
- google-auth-httplib2=0.0.4
- google-cloud-core=1.4.3
- google-cloud-storage=1.33.0
- google-crc32c=1.0.0
- google-resumable-media=1.1.0
- googleapis-common-protos=1.52.0
- graphite2=1.3.13
- graphviz=2.42.3
- grpcio=1.34.0
- gsl=2.6
- gxx_impl_linux-64=7.5.0
- gxx_linux-64=7.5.0
- harfbuzz=2.7.2
- hmmer=3.3.1
- htseq=0.12.4
- htslib=1.11
- httplib2=0.18.1
- icu=67.1
- idba=1.1.3
- idna=2.10
- imagemagick=7.0.10_28
- importlib-metadata=3.1.1
- importlib_metadata=3.1.1
- iniconfig=1.1.1
- ipython_genutils=0.2.0
- jbig=2.1
- jdcal=1.4.1
- jinja2=2.11.2
- jmespath=0.10.0
- joblib=0.17.0
- jpeg=9d
- jsonschema=3.2.0
- jupyter_core=4.7.0
- k8=0.2.5
- keggcharter=0.2.1
- kernel-headers_linux-64=2.6.32
- kiwisolver=1.3.1
- krb5=1.17.2
- krona=2.7.1
- lcms2=2.11
- ld_impl_linux-64=2.35.1
- libapr=1.6.5
- libapriconv=1.2.2
- libaprutil=1.6.1
- libblas=3.8.0
- libcblas=3.8.0
- libcrc32c=1.1.1
- libcurl=7.71.1
- libdeflate=1.6
- libedit=3.1.20191231
- libev=4.33
- libffi=3.3
- libgcc=7.2.0
- libgcc-ng=9.3.0
- libgd=2.2.5
- libgfortran-ng=7.5.0
- libgfortran4=7.5.0
- libglib=2.66.3
- libgomp=9.3.0
- libiconv=1.16
- libidn2=2.3.0
- liblapack=3.8.0
- libnghttp2=1.41.0
- libntlm=1.4
- libopenblas=0.3.10
- libpng=1.6.37
- libprotobuf=3.13.0.1
- librsvg=2.50.2
- libsodium=1.0.18
- libssh2=1.9.0
- libstdcxx-ng=9.3.0
- libtiff=4.1.0
- libtool=2.4.6
- libunistring=0.9.10
- libutf8proc=2.1.1
- libuuid=2.32.1
- libwebp=1.1.0
- libwebp-base=1.1.0
- libxcb=1.13
- libxml2=2.9.10
- libxslt=1.1.33
- llvm-meta=7.0.0
- logmuse=0.2.6
- lxml=4.6.2
- lz4-c=1.8.3
- make=4.3
- markupsafe=1.1.1
- matplotlib-base=3.3.3
- maxbin2=2.2.7
- maxquant=1.6.10.43
- megahit=1.2.9
- minimap2=2.17
- mono=5.14.0.177
- more-itertools=8.6.0
- mosca=1.2.1
- multidict=4.7.5
- nbformat=5.0.8
- ncurses=6.2
- networkx=2.5
- numpy=1.19.4
- oauth2client=4.1.3
- olefile=0.46
- openjdk=11.0.8
- openjpeg=2.3.1
- openmp=7.0.0
- openpyxl=3.0.5
- openssl=1.1.1j
- packaging=20.8
- pandas=1.1.4
- pango=1.42.4
- paramiko=2.7.2
- pcre=8.44
- pcre2=10.35
- pear=0.9.6
- peppy=0.31.0
- perl=5.26.2
- perl-app-cpanminus=1.7044
- perl-archive-tar=2.32
- perl-autoloader=5.74
- perl-base=2.23
- perl-business-isbn=3.004
- perl-business-isbn-data=20140910.003
- perl-carp=1.38
- perl-clone=0.42
- perl-common-sense=3.74
- perl-compress-raw-bzip2=2.087
- perl-compress-raw-zlib=2.087
- perl-config-general=2.63
- perl-constant=1.33
- perl-data-dumper=2.173
- perl-digest-hmac=1.03
- perl-digest-md5=2.55
- perl-digest-perl-md5=1.9
- perl-dynaloader=1.25
- perl-encode=2.88
- perl-encode-locale=1.05
- perl-exporter=5.72
- perl-exporter-tiny=1.002001
- perl-extutils-makemaker=7.36
- perl-file-listing=6.04
- perl-file-path=2.16
- perl-file-temp=0.2304
- perl-font-ttf=1.06
- perl-gd=2.71
- perl-html-parser=3.72
- perl-html-tagset=3.20
- perl-html-tree=5.07
- perl-http-cookies=6.04
- perl-http-daemon=6.01
- perl-http-date=6.02
- perl-http-message=6.18
- perl-http-negotiate=6.01
- perl-io-compress=2.087
- perl-io-html=1.001
- perl-io-socket-ssl=2.066
- perl-io-string=1.08
- perl-io-zlib=1.10
- perl-json=4.02
- perl-json-xs=2.34
- perl-libwww-perl=6.39
- perl-list-moreutils=0.428
- perl-list-moreutils-xs=0.428
- perl-lwp-mediatypes=6.04
- perl-lwp-protocol-https=6.07
- perl-lwp-simple=6.15
- perl-math-bezier=0.01
- perl-math-round=0.07
- perl-math-vecstat=0.08
- perl-mime-base64=3.15
- perl-module-implementation=0.09
- perl-module-runtime=0.016
- perl-mozilla-ca=20180117
- perl-net-http=6.19
- perl-net-ssleay=1.88
- perl-ntlm=1.09
- perl-number-format=1.75
- perl-params-validate=1.29
- perl-parent=0.236
- perl-pathtools=3.75
- perl-readonly=2.05
- perl-regexp-common=2017060201
- perl-scalar-list-utils=1.52
- perl-set-intspan=1.19
- perl-socket=2.027
- perl-statistics-basic=1.6611
- perl-storable=3.15
- perl-svg=2.84
- perl-test-requiresinternet=0.05
- perl-text-format=0.59
- perl-time-hires=1.9760
- perl-time-local=1.28
- perl-try-tiny=0.30
- perl-types-serialiser=1.0
- perl-uri=1.76
- perl-www-robotrules=6.02
- perl-xml-namespacesupport=1.12
- perl-xml-parser=2.44_01
- perl-xml-sax=1.02
- perl-xml-sax-base=1.09
- perl-xml-sax-expat=0.51
- perl-xml-simple=2.25
- perl-xsloader=0.24
- pillow=8.0.1
- pip=20.3.1
- pixman=0.40.0
- pkg-config=0.29.2
- pluggy=0.13.1
- pplacer=1.1.alpha19
- prettytable=2.0.0
- prodigal=2.6.3
- progressbar=2.5
- progressbar33=2.4
- protobuf=3.13.0.1
- psutil=5.7.3
- pthread-stubs=0.4
- pulp=2.3.1
- py=1.10.0
- pyasn1=0.4.8
- pyasn1-modules=0.2.7
- pycparser=2.20
- pygments=2.7.2
- pygraphviz=1.6
- pynacl=1.4.0
- pyopenssl=20.0.0
- pyparsing=2.4.7
- pyrsistent=0.17.3
- pysam=0.16.0.1
- pysftp=0.2.9
- pysocks=1.7.1
- pytest=6.2.2
- python=3.7.8
- python-dateutil=2.8.1
- python-irodsclient=0.8.2
- python_abi=3.7
- pytz=2020.4
- pyyaml=5.3.1
- quast=5.0.2
- r-askpass=1.1
- r-assertthat=0.2.1
- r-backports=1.2.0
- r-base=4.0.3
- r-bh=1.72.0_3
- r-biocmanager=1.30.10
- r-bit=4.0.4
- r-bit64=4.0.5
- r-bitops=1.0_6
- r-blob=1.2.1
- r-brio=1.1.0
- r-callr=3.5.1
- r-catools=1.18.0
- r-cli=2.2.0
- r-colorspace=2.0_0
- r-crayon=1.3.4
- r-curl=4.3
- r-dbi=1.1.0
- r-desc=1.2.0
- r-diffobj=0.3.2
- r-digest=0.6.27
- r-ellipsis=0.3.1
- r-evaluate=0.14
- r-fansi=0.4.1
- r-farver=2.0.3
- r-formatr=1.7
- r-futile.logger=1.4.3
- r-futile.options=1.0.1
- r-getopt=1.20.3
- r-ggplot2=3.3.2
- r-glue=1.4.2
- r-gplots=3.1.1
- r-gtable=0.3.0
- r-gtools=3.8.2
- r-httr=1.4.2
- r-isoband=0.2.3
- r-jsonlite=1.7.1
- r-kernsmooth=2.23_18
- r-labeling=0.4.2
- r-lambda.r=1.2.4
- r-lattice=0.20_41
- r-lifecycle=0.2.0
- r-locfit=1.5_9.4
- r-magrittr=2.0.1
- r-mass=7.3_53
- r-matrix=1.2_18
- r-matrixstats=0.57.0
- r-memoise=1.1.0
- r-mgcv=1.8_33
- r-mime=0.9
- r-munsell=0.5.0
- r-nlme=3.1_150
- r-openssl=1.4.3
- r-optparse=1.6.6
- r-pheatmap=1.0.12
- r-pillar=1.4.7
- r-pkgbuild=1.1.0
- r-pkgconfig=2.0.3
- r-pkgload=1.1.0
- r-plogr=0.2.0
- r-praise=1.0.0
- r-prettyunits=1.1.1
- r-processx=3.4.5
- r-ps=1.4.0
- r-r6=2.5.0
- r-rcolorbrewer=1.1_2
- r-rcpp=1.0.5
- r-rcpparmadillo=0.10.1.2.0
- r-rcurl=1.98_1.2
- r-rematch2=2.1.2
- r-rlang=0.4.9
- r-rprojroot=2.0.2
- r-rsqlite=2.2.1
- r-rstudioapi=0.13
- r-scales=1.1.1
- r-snow=0.4_3
- r-survival=3.2_7
- r-sys=3.4
- r-testthat=3.0.0
- r-tibble=3.0.4
- r-utf8=1.1.4
- r-vctrs=0.3.5
- r-viridislite=0.3.0
- r-waldo=0.2.3
- r-withr=2.3.0
- r-xml=3.99_0.3
- r-xtable=1.8_4
- r-zeallot=0.1.0
- ratelimiter=1.2.0
- readline=8.0
- recognizer=1.4.1
- reportlab=3.5.56
- requests=2.25.0
- rsa=4.6
- s3transfer=0.3.3
- samtools=1.11
- scikit-learn=0.23.2
- scipy=1.5.3
- sed=4.8
- seqkit=0.14.0
- seqtk=1.3
- serf=1.3.9
- setuptools=49.6.0
- simplejson=3.17.2
- six=1.15.0
- slacker=0.14.0
- smmap=3.0.4
- snakemake=5.32.0
- snakemake-minimal=5.32.0
- sortmerna=2.1b
- spades=3.14.1
- sqlite=3.34.0
- svn=1.10.2
- sysroot_linux-64=2.12
- tar=1.32
- tbb=2020.2
- threadpoolctl=2.1.0
- tk=8.6.10
- tktable=2.10
- toml=0.10.2
- toposort=1.5
- tornado=6.1
- tqdm=4.54.0
- traitlets=5.0.5
- trimmomatic=0.39
- typing-extensions=3.7.4.3
- typing_extensions=3.7.4.3
- ubiquerg=0.6.1
- upimapi=1.1.2
- uritemplate=3.0.1
- urllib3=1.25.11
- veracitools=0.1.3
- wcwidth=0.2.5
- wget=1.20.1
- wheel=0.36.0
- wrapt=1.12.1
- xlrd=1.2.0
- xlsxwriter=1.3.7
- xmlrunner=1.7.7
- xorg-fixesproto=5.0
- xorg-inputproto=2.3.2
- xorg-kbproto=1.0.7
- xorg-libice=1.0.10
- xorg-libsm=1.2.3
- xorg-libx11=1.6.12
- xorg-libxau=1.0.9
- xorg-libxdmcp=1.1.3
- xorg-libxext=1.3.4
- xorg-libxfixes=5.0.3
- xorg-libxi=1.7.10
- xorg-libxpm=3.5.13
- xorg-libxrender=0.9.10
- xorg-libxt=1.1.5
- xorg-libxtst=1.2.3
- xorg-recordproto=1.14.2
- xorg-renderproto=0.11.1
- xorg-xextproto=7.3.0
- xorg-xproto=7.0.31
- xz=5.2.5
- yaml=0.2.5
- yarl=1.5.1
- zipp=3.4.0
- zlib=1.2.11
- zstd=1.4.4
......@@ -86,7 +86,7 @@ about:
Peptide-to-Spectrum matching, with the annotated ORFs as reference database.
Final steps include differential expression analysis for both MT and MP, and
metabolic pathways analysis through KEGG Pathways.
doc_url: https://github.com/iquasere/MOSCA/blob/master/README.md
doc_url: https://github.com/iquasere/MOSCA/wiki
dev_url: https://github.com/iquasere/MOSCA
extra:
......
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