diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md new file mode 100644 index 0000000..aabd7ab --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -0,0 +1,24 @@ +--- +name: Bug report +about: Create a report to help us improve +title: "[BUG]" +labels: '' +assignees: '' + +--- + +**Describe the bug** +A clear and concise description of what the bug is. + +**To Reproduce** +Steps to reproduce the behavior, is needed a link to the samples causing the problem + +**Expected behavior** +A clear and concise description of what you expected to happen. + + **Environment:** + - OS: [e.g. Ubuntu 18.04] +- Dadaist2 version: + +**Additional context** +Add any other context about the problem here. diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md new file mode 100644 index 0000000..4449952 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -0,0 +1,17 @@ +--- +name: Feature request +about: Suggest an idea for this project +title: '' +labels: '' +assignees: '' + +--- + +**Is your feature request related to a problem? Please describe.** +A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] + +**Describe the solution you'd like** +A clear and concise description of what you want to happen. + +**Additional context** +Add any other context or screenshots about the feature request here. diff --git a/docs/dadaist2-1.1.yaml b/docs/dadaist2-1.1.yaml new file mode 100644 index 0000000..b876dba --- /dev/null +++ b/docs/dadaist2-1.1.yaml @@ -0,0 +1,287 @@ +channels: +- bioconda +- conda-forge +- defaults +dependencies: +- _r-mutex=1.0.1 +- argtable2=2.13 +- bioconductor-biobase=2.50.0 +- bioconductor-biocgenerics=0.36.0 +- bioconductor-biocparallel=1.24.1 +- bioconductor-biomformat=1.18.0 +- bioconductor-biostrings=2.58.0 +- bioconductor-dada2=1.18.0 +- bioconductor-decipher=2.18.1 +- bioconductor-delayedarray=0.16.3 +- bioconductor-genomeinfodb=1.26.4 +- bioconductor-genomeinfodbdata=1.2.4 +- bioconductor-genomicalignments=1.26.0 +- bioconductor-genomicranges=1.42.0 +- bioconductor-iranges=2.24.1 +- bioconductor-matrixgenerics=1.2.1 +- bioconductor-microbiome=1.12.0 +- bioconductor-multtest=2.46.0 +- bioconductor-phyloseq=1.34.0 +- bioconductor-rhdf5=2.34.0 +- bioconductor-rhdf5filters=1.2.0 +- bioconductor-rhdf5lib=1.12.1 +- bioconductor-rhtslib=1.22.0 +- bioconductor-rsamtools=2.6.0 +- bioconductor-s4vectors=0.28.1 +- bioconductor-shortread=1.48.0 +- bioconductor-summarizedexperiment=1.20.0 +- bioconductor-xvector=0.30.0 +- bioconductor-zlibbioc=1.36.0 +- biom-format=2.1.10 +- bwidget=1.9.14 +- bzip2=1.0.8 +- c-ares=1.17.1 +- ca-certificates=2021.7.5 +- cached-property=1.5.2 +- cached_property=1.5.2 +- cairo=1.16.0 +- cctools_osx-64=949.0.1 +- certifi=2021.5.30 +- clang=11.1.0 +- clang-11=11.1.0 +- clang_osx-64=11.1.0 +- clangxx=11.1.0 +- clangxx_osx-64=11.1.0 +- click=8.0.1 +- clustalo=1.2.4 +- colorama=0.4.4 +- commonmark=0.9.1 +- compiler-rt=11.1.0 +- compiler-rt_osx-64=11.1.0 +- curl=7.77.0 +- cutadapt=3.4 +- cycler=0.10.0 +- dadaist2=1.0.2 +- dnaio=0.5.1 +- fastp=0.20.1 +- fasttree=2.1.10 +- font-ttf-dejavu-sans-mono=2.37 +- font-ttf-inconsolata=3.000 +- font-ttf-source-code-pro=2.038 +- font-ttf-ubuntu=0.83 +- fontconfig=2.13.1 +- fonts-conda-ecosystem=1 +- fonts-conda-forge=1 +- freetype=2.10.4 +- fribidi=1.0.10 +- future=0.18.2 +- gettext=0.21.0 +- gfortran_impl_osx-64=9.3.0 +- gfortran_osx-64=9.3.0 +- gmp=6.2.1 +- graphite2=1.3.14 +- gsl=2.6 +- h5py=3.2.1 +- harfbuzz=2.8.1 +- hdf5=1.10.6 +- icu=68.1 +- isa-l=2.30.0 +- isl=0.22.1 +- jbig=2.1 +- jpeg=9d +- kiwisolver=1.3.1 +- krb5=1.19.1 +- lcms2=2.12 +- ld64_osx-64=530 +- ldid=2.1.2 +- lerc=2.2.1 +- libblas=3.9.0 +- libcblas=3.9.0 +- libclang-cpp11.1=11.1.0 +- libcurl=7.77.0 +- libcxx=11.1.0 +- libdeflate=1.7 +- libedit=3.1.20210216 +- libev=4.33 +- libffi=3.3 +- libgfortran=5.0.0 +- libgfortran-devel_osx-64=9.3.0 +- libgfortran5=9.3.0 +- libglib=2.68.3 +- libiconv=1.16 +- liblapack=3.9.0 +- libllvm11=11.1.0 +- libllvm12=12.0.0 +- libnghttp2=1.43.0 +- libopenblas=0.3.15 +- libpng=1.6.37 +- libssh2=1.9.0 +- libtiff=4.3.0 +- libwebp-base=1.2.0 +- libxml2=2.9.12 +- libzip=1.7.3 +- llvm-openmp=11.1.0 +- llvm-tools=11.1.0 +- lz4-c=1.9.3 +- make=4.3 +- matplotlib-base=3.4.2 +- mpc=1.1.0 +- mpfr=4.0.2 +- ncurses=6.2 +- numpy=1.20.3 +- olefile=0.46 +- openjpeg=2.4.0 +- openssl=1.1.1k +- pandas=1.2.4 +- pango=1.48.5 +- patsy=0.5.1 +- pcre=8.45 +- pcre2=10.36 +- perl=5.26.2 +- perl-capture-tiny=0.48 +- perl-carp=1.38 +- perl-exporter=5.72 +- perl-extutils-makemaker=7.36 +- perl-fastx-reader=1.0.5 +- pigz=2.6 +- pip=21.1.2 +- pixman=0.40.0 +- pygments=2.9.0 +- pyparsing=2.4.7 +- python=3.9.5 +- python-dateutil=2.8.1 +- python-isal=0.10.0 +- python_abi=3.9 +- pytz=2021.1 +- pyyaml=5.4.1 +- qax=0.9.2 +- r-ade4=1.7_17 +- r-ape=5.5 +- r-assertthat=0.2.1 +- r-backports=1.2.1 +- r-base=4.0.5 +- r-bh=1.75.0_0 +- r-bit=4.0.4 +- r-bit64=4.0.5 +- r-bitops=1.0_7 +- r-blob=1.2.1 +- r-brio=1.1.2 +- r-cachem=1.0.5 +- r-callr=3.7.0 +- r-cli=2.5.0 +- r-cluster=2.1.2 +- r-codetools=0.2_18 +- r-colorspace=2.0_1 +- r-crayon=1.4.1 +- r-data.table=1.14.0 +- r-dbi=1.1.1 +- r-desc=1.3.0 +- r-diffobj=0.3.4 +- r-digest=0.6.27 +- r-dplyr=1.0.6 +- r-ellipsis=0.3.2 +- r-evaluate=0.14 +- r-fansi=0.5.0 +- r-farver=2.1.0 +- r-fastmap=1.1.0 +- r-foreach=1.5.1 +- r-formatr=1.11 +- r-futile.logger=1.4.3 +- r-futile.options=1.0.1 +- r-generics=0.1.0 +- r-ggplot2=3.3.4 +- r-glue=1.4.2 +- r-gtable=0.3.0 +- r-hms=1.1.0 +- r-hwriter=1.3.2 +- r-igraph=1.2.6 +- r-isoband=0.2.4 +- r-iterators=1.0.13 +- r-jpeg=0.1_8.1 +- r-jsonlite=1.7.2 +- r-labeling=0.4.2 +- r-lambda.r=1.2.4 +- r-lattice=0.20_44 +- r-latticeextra=0.6_29 +- r-lifecycle=1.0.0 +- r-magrittr=2.0.1 +- r-mass=7.3_54 +- r-matrix=1.3_2 +- r-matrixstats=0.59.0 +- r-memoise=2.0.0 +- r-mgcv=1.8_36 +- r-munsell=0.5.0 +- r-nlme=3.1_152 +- r-permute=0.9_5 +- r-pillar=1.6.1 +- r-pixmap=0.4_12 +- r-pkgconfig=2.0.3 +- r-pkgload=1.2.1 +- r-plogr=0.2.0 +- r-plyr=1.8.6 +- r-png=0.1_7 +- r-praise=1.0.0 +- r-prettyunits=1.1.1 +- r-processx=3.5.2 +- r-progress=1.2.2 +- r-ps=1.6.0 +- r-purrr=0.3.4 +- r-r6=2.5.0 +- r-rcolorbrewer=1.1_2 +- r-rcpp=1.0.6 +- r-rcppparallel=5.1.4 +- r-rcurl=1.98_1.3 +- r-rematch2=2.1.2 +- r-reshape2=1.4.4 +- r-rlang=0.4.11 +- r-rprojroot=2.0.2 +- r-rsqlite=2.2.5 +- r-rstudioapi=0.13 +- r-rtsne=0.15 +- r-scales=1.1.1 +- r-snow=0.4_3 +- r-sp=1.4_5 +- r-stringi=1.6.2 +- r-stringr=1.4.0 +- r-survival=3.2_11 +- r-testthat=3.0.3 +- r-tibble=3.1.2 +- r-tidyr=1.1.3 +- r-tidyselect=1.1.1 +- r-utf8=1.2.1 +- r-vctrs=0.3.8 +- r-vegan=2.5_7 +- r-viridislite=0.4.0 +- r-waldo=0.2.5 +- r-withr=2.4.2 +- readline=8.1 +- rich=10.6.0 +- scipy=1.6.3 +- seaborn=0.11.1 +- seaborn-base=0.11.1 +- seqfu=1.3.3 +- setuptools=52.0.0 +- six=1.16.0 +- sqlite=3.35.5 +- statsmodels=0.12.2 +- tapi=1100.0.11 +- tk=8.6.10 +- tktable=2.10 +- tornado=6.1 +- typing_extensions=3.10.0.0 +- tzdata=2021a +- wheel=0.36.2 +- xopen=1.1.0 +- xz=5.2.5 +- yaml=0.2.5 +- zip=3.0 +- zlib=1.2.11 +- zstd=1.5.0 +- pip: + - asgiref==3.3.4 + - biopython==1.79 + - decorator==4.4.2 + - django==3.2.4 + - illumina-utils==2.11 + - networkx==2.5.1 + - oligotyping==3.1 + - pillow==8.2.0 + - python-levenshtein==0.12.2 + - sqlparse==0.4.1 +name: dada0 +