From ab9601906833a11a7c9ef5faaa827be332900ac8 Mon Sep 17 00:00:00 2001 From: Laura Cook <l.cook2@student.unimelb.edu.au> Date: Wed, 23 Sep 2020 19:57:50 +1000 Subject: [PATCH] first commit of conda environment with packages for whole genome alignment --- cross_species_comparison/env/wga.yaml | 153 ++++++++++++++++++++++++++ 1 file changed, 153 insertions(+) create mode 100644 cross_species_comparison/env/wga.yaml diff --git a/cross_species_comparison/env/wga.yaml b/cross_species_comparison/env/wga.yaml new file mode 100644 index 0000000..96fbe71 --- /dev/null +++ b/cross_species_comparison/env/wga.yaml @@ -0,0 +1,153 @@ +name: wga +channels: + - bioconda + - biocore + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1=conda_forge + - _openmp_mutex=4.5=1_gnu + - bzip2=1.0.8=h516909a_3 + - c-ares=1.11.0=h470a237_1 + - ca-certificates=2020.6.20=hecda079_0 + - cairo=1.16.0=h3fc0475_1005 + - cd-hit=4.8.1=h8b12597_3 + - certifi=2020.6.20=py38h32f6830_0 + - curl=7.71.1=he644dc0_6 + - entrez-direct=13.9=pl526h375a9b1_0 + - expat=2.2.9=he1b5a44_2 + - fontconfig=2.13.1=h1056068_1002 + - freetype=2.10.2=he06d7ca_0 + - fribidi=1.0.10=h516909a_0 + - genometools-genometools=1.6.1=py38h23571c4_2 + - gettext=0.19.8.1=hc5be6a0_1002 + - glib=2.66.0=h0dae87d_0 + - gmp=6.1.2=hf484d3e_1000 + - gnutls=3.5.19=h2a4e5f8_1 + - graphite2=1.3.13=he1b5a44_1001 + - harfbuzz=2.7.2=hee91db6_0 + - hmmer=3.3.1=he1b5a44_0 + - icu=67.1=he1b5a44_0 + - krb5=1.17.1=hfafb76e_3 + - ld_impl_linux-64=2.35=h769bd43_9 + - libcurl=7.71.1=hcdd3856_6 + - libedit=3.1.20191231=he28a2e2_2 + - libev=4.33=h516909a_1 + - libffi=3.2.1=he1b5a44_1007 + - libgcc-ng=9.3.0=h24d8f2e_16 + - libgomp=9.3.0=h24d8f2e_16 + - libiconv=1.16=h516909a_0 + - libnghttp2=1.41.0=hab1572f_1 + - libpng=1.6.37=hed695b0_2 + - libssh2=1.9.0=hab1572f_5 + - libstdcxx-ng=9.3.0=hdf63c60_16 + - libuuid=2.32.1=h14c3975_1000 + - libxcb=1.13=h14c3975_1002 + - libxml2=2.9.10=h68273f3_2 + - llvm-openmp=8.0.1=hc9558a2_0 + - ltr_retriever=2.9.0=0 + - mafft=7.471=h516909a_0 + - ncurses=6.2=he1b5a44_1 + - nettle=3.3=0 + - nseg=1.0.1=h516909a_0 + - openmp=8.0.1=0 + - openssl=1.1.1h=h516909a_0 + - pango=1.42.4=h7062337_4 + - pcre=8.44=he1b5a44_0 + - perl=5.26.2=h516909a_1006 + - perl-app-cpanminus=1.7044=pl526_1 + - perl-archive-tar=2.32=pl526_0 + - perl-base=2.23=pl526_1 + - perl-business-isbn=3.004=pl526_0 + - perl-business-isbn-data=20140910.003=pl526_0 + - perl-carp=1.38=pl526_3 + - perl-common-sense=3.74=pl526_2 + - perl-compress-raw-bzip2=2.087=pl526he1b5a44_0 + - perl-compress-raw-zlib=2.087=pl526hc9558a2_0 + - perl-constant=1.33=pl526_1 + - perl-data-dumper=2.173=pl526_0 + - perl-digest-hmac=1.03=pl526_3 + - perl-digest-md5=2.55=pl526_0 + - perl-encode=2.88=pl526_1 + - perl-encode-locale=1.05=pl526_6 + - perl-exporter=5.72=pl526_1 + - perl-exporter-tiny=1.002001=pl526_0 + - perl-extutils-makemaker=7.36=pl526_1 + - perl-file-listing=6.04=pl526_1 + - perl-file-path=2.16=pl526_0 + - perl-file-temp=0.2304=pl526_2 + - perl-file-which=1.23=pl526_0 + - perl-html-parser=3.72=pl526h6bb024c_5 + - perl-html-tagset=3.20=pl526_3 + - perl-html-tree=5.07=pl526_1 + - perl-http-cookies=6.04=pl526_0 + - perl-http-daemon=6.01=pl526_1 + - perl-http-date=6.02=pl526_3 + - perl-http-message=6.18=pl526_0 + - perl-http-negotiate=6.01=pl526_3 + - perl-io-compress=2.087=pl526he1b5a44_0 + - perl-io-html=1.001=pl526_2 + - perl-io-socket-ssl=2.066=pl526_0 + - perl-io-zlib=1.10=pl526_2 + - perl-json=4.02=pl526_0 + - perl-json-xs=2.34=pl526h6bb024c_3 + - perl-libwww-perl=6.39=pl526_0 + - perl-list-moreutils=0.428=pl526_1 + - perl-list-moreutils-xs=0.428=pl526_0 + - perl-lwp-mediatypes=6.04=pl526_0 + - perl-lwp-protocol-https=6.07=pl526_4 + - perl-mime-base64=3.15=pl526_1 + - perl-mozilla-ca=20180117=pl526_1 + - perl-net-http=6.19=pl526_0 + - perl-net-ssleay=1.88=pl526h90d6eec_0 + - perl-ntlm=1.09=pl526_4 + - perl-parent=0.236=pl526_1 + - perl-pathtools=3.75=pl526h14c3975_1 + - perl-scalar-list-utils=1.52=pl526h516909a_0 + - perl-socket=2.027=pl526_1 + - perl-storable=3.15=pl526h14c3975_0 + - perl-test-requiresinternet=0.05=pl526_0 + - perl-text-soundex=3.05=pl526_1000 + - perl-time-local=1.28=pl526_1 + - perl-try-tiny=0.30=pl526_1 + - perl-types-serialiser=1.0=pl526_2 + - perl-uri=1.76=pl526_0 + - perl-www-robotrules=6.02=pl526_3 + - perl-xml-namespacesupport=1.12=pl526_0 + - perl-xml-parser=2.44=pl526h4e0c4b3_7 + - perl-xml-sax=1.02=pl526_0 + - perl-xml-sax-base=1.09=pl526_0 + - perl-xml-sax-expat=0.51=pl526_3 + - perl-xml-simple=2.25=pl526_1 + - perl-xsloader=0.24=pl526_0 + - pip=20.2.3=py_0 + - pixman=0.38.0=h516909a_1003 + - pthread-stubs=0.4=h14c3975_1001 + - python=3.8.5=h1103e12_8_cpython + - python_abi=3.8=1_cp38 + - readline=8.0=he28a2e2_2 + - recon=1.08=h516909a_2 + - repeatmasker=4.1.0=pl526_0 + - repeatmodeler=2.0.1=pl526_0 + - repeatscout=1.0.6=h516909a_1 + - rmblast=2.9.0=h2d02072_0 + - setuptools=49.6.0=py38h32f6830_1 + - sqlite=3.33.0=h4cf870e_0 + - tk=8.6.10=hed695b0_0 + - trf=4.09.1=h516909a_0 + - wheel=0.35.1=pyh9f0ad1d_0 + - xorg-kbproto=1.0.7=h14c3975_1002 + - xorg-libice=1.0.10=h516909a_0 + - xorg-libsm=1.2.3=h84519dc_1000 + - xorg-libx11=1.6.12=h516909a_0 + - xorg-libxau=1.0.9=h14c3975_0 + - xorg-libxdmcp=1.1.3=h516909a_0 + - xorg-libxext=1.3.4=h516909a_0 + - xorg-libxrender=0.9.10=h516909a_1002 + - xorg-renderproto=0.11.1=h14c3975_1002 + - xorg-xextproto=7.3.0=h14c3975_1002 + - xorg-xproto=7.0.31=h14c3975_1007 + - xz=5.2.5=h516909a_1 + - zlib=1.2.11=h516909a_1009 +prefix: /home/lecook/.conda/envs/wga + -- GitLab