metaWRAP v=0.4

bxlab · Dec 4, 2017 · 2e9b4b6 · 2e9b4b6
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diff --git 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
@@ -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
@@ -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
+