From 2e9b4b6b4260ed99e51cf9ed220dfd8aa925bb74 Mon Sep 17 00:00:00 2001 From: German Uritskiy Date: Mon, 4 Dec 2017 16:57:28 -0500 Subject: [PATCH] metaWRAP v=0.4 --- README.md | 2 +- dependancies.txt | 90 +++++++++++++++++++++++++++++ environment.yml | 143 +++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 234 insertions(+), 1 deletion(-) create mode 100644 dependancies.txt create mode 100644 environment.yml diff --git a/README.md b/README.md index 78c8f47..00b1d7b 100755 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ # metaWRAP - Comprehensive Metagenome Analysis in One Place -## metaWRAP version 0.4 +## metaWRAP v=0.4 metaWRAP aims to be an easy-to-use inclusive wrapper program that accomplishes the most basic tasks in metagenomic analysis: QC, assembly, binning, visualization, and taxonomic profiling. While there is no single best approach for processing metagenomic data, metaWRAP is meant to be a fast and simple first pass program before you delve deeper into parameterization of your approach. Each individual component of the pipeline is also a standalone module. This modularity allows the users to use only the modules they are interested in. diff --git a/dependancies.txt b/dependancies.txt new file mode 100644 index 0000000..5d201a5 --- /dev/null +++ b/dependancies.txt @@ -0,0 +1,90 @@ +#ALL DEPENDANCIES: +-BLAST 2.6.0+ +-bmtagger 3.101 +-Bowtie2 2.3.2 +-bwa 0.7.15-r1140 +-Checkm v1.0.7 +-FastQC v0.11.5 +-kraken 0.10.6 +-kronatools 2.7 +-megahit v1.1.1-2-g02102e1 +-metabat2 2.9.1 +-concoct 0.4.0 +-MaxBin2 2.2.4 +-perl v5.22.0 +-python2.7 +-quast v4.5 +-R 3.3.2 +-ggplot2 +-samtools 1.3.1 +-SPAdes v3.10.1 +-trim_galore 0.4.3 +-python 2.7 +-seaborn 0.8.1 +-salmon +-matplotlib + + +#DATABASES: +1.4GB Checkm_DB (past of CheckM installation) +161GB -KRAKEN standard database +71GB RefSeq NCBI_nt +283MB RefSeq NCBI_tax +20GB Indexed hg38 (for bmtagger) + + +#More detailed dependancies: + +general: +-python2.7 + +read_qc.sh +-fastqc v0.11.5 +-trim_galore 0.4.3 +-bmtagger 3.101 +-human_db hg38 + +assembly.sh +-SPAdes v3.10.1 +-bwa 0.7.15-r1140 +-megahit v1.1.1-2-g02102e1 +-quast v4.5 + +binning.sh +-bwa 0.7.15-r1140 +-samtools 1.3.1 +-metabat2 2.9.1 +-concoct 0.4.0 +-MaxBin2 2.2.4 + +bin_refinement.sh +-python 2.7 +-matplotlib +-checkm v1.0.7 +-checkm_DB (standard) + +reassemble_bins.sh +-bwa 0.7.15-r1140 +-samtools 1.3.1 +-checkm v1.0.7 +-checkm_DB (standard) +-SPAdes 3.11.1 + +quant_bins.sh +-salmon +-seaborn 0.8.1 + +blobology.sh +-refseq_db NCBI_nt +-refseq_db NCBI_tax +-blast 2.6.0+ +-bowtie2 2.3.2 +-perl v5.22.0 +-R 3.3.2 +-ggplot2 + +kraken.sh +-kraken 0.10.6 +-kraken_db STANDARD_DATABASE +-kronatools 2.7 + diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..c7c4b9a --- /dev/null +++ b/environment.yml @@ -0,0 +1,143 @@ +name: metawrap +channels: +- bioconda +- r +- defaults +- conda-forge +dependencies: +- bcftools=1.3.1=1 +- biopython=1.69=np110py27_0 +- blast=2.7.1=boost1.64_1 +- bmfilter=3.101=1 +- bmtagger=3.101=3 +- bmtool=3.101=1 +- bowtie2=2.3.0=py27_1 +- bwa=0.7.15=1 +- checkm-genome=1.0.7=py27_0 +- concoct=0.4.0=gsl1.16_0 +- cutadapt=1.15=py27_0 +- dendropy=4.2.0=py27_0 +- extract_fullseq=3.101=2 +- fastqc=0.11.5=1 +- ggplot=0.6.8=py27_0 +- htslib=1.3=0 +- java-jdk=8.0.92=1 +- jemalloc=4.5.0=0 +- kraken=0.10.6_eaf8fb68=2 +- megahit=1.1.2=py27_0 +- mmtf-python=1.0.2=py27_0 +- perl-threaded=5.22.0=10 +- pysam=0.9.0=py27_1 +- python-dateutil=2.3=py27_0 +- quast=4.1=py27_0 +- salmon=0.9.1=0 +- samtools=1.6=0 +- screamingbackpack=0.2.333=py27_0 +- simplejson=3.8.1=py27_0 +- srprism=2.4.24=2 +- tbb=4.4_20150728=0 +- trim-galore=0.4.5=pl5.22.0_0 +- typing=3.5.2.2=py27_0 +- xopen=0.3.2=py27_0 +- boost=1.64.0=py27_4 +- boost-cpp=1.64.0=1 +- brewer2mpl=1.4.1=py27_2 +- gnutls=3.5.15=0 +- gsl=1.16=0 +- libidn11=1.33=0 +- nettle=3.3=0 +- perl=5.22.0.1=0 +- pyqt=4.11.4=py27_2 +- alabaster=0.7.10=py27he5a193a_0 +- asn1crypto=0.23.0=py27h7b0c810_0 +- babel=2.5.0=py27h20693cd_0 +- backports=1.0=py27h63c9359_1 +- backports_abc=0.5=py27h7b3c97b_0 +- bz2file=0.98=py27_0 +- bzip2=1.0.6=h6d464ef_2 +- ca-certificates=2017.08.26=h1d4fec5_0 +- cairo=1.14.8=0 +- certifi=2017.11.5=py27h71e7faf_0 +- cffi=1.11.2=py27ha7929c6_0 +- chardet=3.0.4=py27hfa10054_1 +- cryptography=2.1.4=py27h6697b16_0 +- curl=7.52.1=0 +- cycler=0.10.0=py27hc7354d3_0 +- cython=0.27.3=py27hc56b35e_0 +- docutils=0.14=py27hae222c1_0 +- enum34=1.1.6=py27h99a27e9_1 +- fontconfig=2.12.1=3 +- freetype=2.5.5=2 +- functools32=3.2.3.2=py27h4ead58f_1 +- gmp=6.1.2=h6c8ec71_1 +- icu=58.2=h9c2bf20_1 +- idna=2.6=py27h5722d68_1 +- imagesize=0.7.1=py27hd17bf80_0 +- intel-openmp=2018.0.0=hc7b2577_8 +- ipaddress=1.0.18=py27h337fd85_0 +- jinja2=2.10=py27h4114e70_0 +- joblib=0.11=py27_0 +- libedit=3.1=heed3624_0 +- libffi=3.2.1=hd88cf55_4 +- libgcc=7.2.0=h69d50b8_2 +- libgcc-ng=7.2.0=h7cc24e2_2 +- libgfortran=3.0.0=1 +- libgfortran-ng=7.2.0=h9f7466a_2 +- libiconv=1.14=0 +- libpng=1.6.30=1 +- libstdcxx-ng=7.2.0=h7a57d05_2 +- libxml2=2.9.4=0 +- markupsafe=1.0=py27h97b2822_1 +- matplotlib=1.5.1=np110py27_0 +- mkl=2018.0.1=h19d6760_4 +- msgpack-python=0.4.8=py27hc2fa789_0 +- ncurses=6.0=h9df7e31_2 +- nose=1.3.7=py27heec2199_2 +- numpy=1.10.2=py27_0 +- openblas=0.2.14=4 +- openssl=1.0.2m=h26d622b_1 +- pandas=0.21.0=py27he307072_1 +- patsy=0.4.1=py27hd1cf8c0_0 +- pcre=8.41=hc27e229_1 +- pip=9.0.1=py27ha730c48_4 +- pixman=0.34.0=hceecf20_3 +- pycairo=1.13.3=py27hea6d626_0 +- pycparser=2.18=py27hefa08c5_1 +- pygments=2.2.0=py27h4a8b6f5_0 +- pyopenssl=17.5.0=py27hcee3be0_0 +- pyparsing=2.2.0=py27hf1513f8_1 +- pysocks=1.6.7=py27he2db6d2_1 +- python=2.7.11=0 +- pytz=2017.3=py27h001bace_0 +- qt=4.8.5=0 +- readline=6.2=2 +- reportlab=3.2.0=py27_0 +- requests=2.18.4=py27hc5b0589_1 +- scikit-learn=0.19.1=py27h445a80a_0 +- scipy=1.0.0=py27hf5f0f52_0 +- seaborn=0.8.1=py27h633ea1e_0 +- setuptools=36.5.0=py27h68b189e_0 +- singledispatch=3.4.0.3=py27h9bcb476_0 +- sip=4.18=py27_0 +- six=1.11.0=py27h5f960f1_1 +- snowballstemmer=1.2.1=py27h44e2768_0 +- sphinx=1.6.3=py27hf9b1778_0 +- sphinx_rtd_theme=0.2.4=py27_0 +- sphinxcontrib=1.0=py27h1512b58_1 +- sphinxcontrib-websupport=1.0.1=py27hf906f22_1 +- sqlite=3.20.1=hb898158_2 +- ssl_match_hostname=3.5.0.1=py27h4ec10b9_2 +- statsmodels=0.8.0=py27hc87d62d_0 +- subprocess32=3.2.7=py27h373dbce_0 +- tk=8.5.18=0 +- tornado=4.5.2=py27h97b179f_0 +- urllib3=1.22=py27ha55213b_0 +- wheel=0.30.0=py27h2bc6bb2_1 +- xz=5.2.3=h55aa19d_2 +- zlib=1.2.8=3 +- pip: + - backports-abc==0.5 + - backports.ssl-match-hostname==3.5.0.1 + - sphinx-rtd-theme==0.2.4 +prefix: /home/guritsk1/miniconda2/envs/metawrap +