From 1cb90a31f3df7741786b757e363115417143a5ee Mon Sep 17 00:00:00 2001 From: "kerchner@gwu.edu" Date: Mon, 15 Sep 2025 00:28:55 -0400 Subject: [PATCH] Updates for Ubuntu 24 --- _episodes/04-assembly.md | 7 +- files/metagenomics-Ubuntu22.yml | 233 ------------------------------ files/metagenomics-Ubuntu24.yml | 247 ++++++++++++++++++++++++++++++++ files/spec-file-Ubuntu22.txt | 231 ----------------------------- files/spec-file-Ubuntu24.txt | 245 +++++++++++++++++++++++++++++++ 5 files changed, 497 insertions(+), 466 deletions(-) delete mode 100644 files/metagenomics-Ubuntu22.yml create mode 100644 files/metagenomics-Ubuntu24.yml delete mode 100644 files/spec-file-Ubuntu22.txt create mode 100644 files/spec-file-Ubuntu24.txt diff --git a/_episodes/04-assembly.md b/_episodes/04-assembly.md index 0b01f637..24ffdba9 100644 --- a/_episodes/04-assembly.md +++ b/_episodes/04-assembly.md @@ -97,7 +97,7 @@ $ metaspades.py {: .bash} ~~~ -SPAdes genome assembler v3.15.0 [metaSPAdes mode] +SPAdes genome assembler v4.2.0 [metaSPAdes mode] Usage: spades.py [options] -o @@ -146,7 +146,10 @@ When the run is finished, it shows this message: SPAdes log can be found here: /home/dcuser/dc_workshop/results/assembly_JC1A/spades.log -Thank you for using SPAdes! +Thank you for using metaSPAdes! If you use it in your research, please cite: + + Nurk, S., Meleshko, D., Korobeynikov, A. and Pevzner, P.A., 2017. metaSPAdes: a new versatile metagenomic assembler. Genome research, 27(5), pp.824-834. + doi.org/10.1101/gr.213959.116 ~~~ {: .bash} diff --git a/files/metagenomics-Ubuntu22.yml b/files/metagenomics-Ubuntu22.yml deleted file mode 100644 index 09822081..00000000 --- a/files/metagenomics-Ubuntu22.yml +++ /dev/null @@ -1,233 +0,0 @@ -name: metagenomics -channels: - - bioconda - - conda-forge - - defaults -dependencies: - - _libgcc_mutex=0.1=conda_forge - - _openmp_mutex=4.5=2_gnu - - _r-mutex=1.0.1=anacondar_1 - - _sysroot_linux-64_curr_repodata_hack=3=h5bd9786_13 - - alsa-lib=1.2.7.2=h166bdaf_0 - - binutils_impl_linux-64=2.36.1=h193b22a_2 - - biom-format=2.1.12=py38h71d37f0_1 - - blast=2.13.0=hf3cf87c_0 - - bowtie2=2.2.5=py38h8c62d01_8 - - brotli=1.0.9=h166bdaf_7 - - brotli-bin=1.0.9=h166bdaf_7 - - bwidget=1.9.14=ha770c72_1 - - bzip2=1.0.8=h7f98852_4 - - c-ares=1.18.1=h7f98852_0 - - ca-certificates=2022.6.15.2=ha878542_0 - - cached-property=1.5.2=hd8ed1ab_1 - - cached_property=1.5.2=pyha770c72_1 - - cairo=1.16.0=ha61ee94_1013 - - certifi=2022.6.15.2=pyhd8ed1ab_0 - - checkm-genome=1.2.1=pyhdfd78af_0 - - click=8.1.3=py38h578d9bd_0 - - curl=7.83.1=h7bff187_0 - - cycler=0.11.0=pyhd8ed1ab_0 - - dendropy=4.5.2=pyh3252c3a_0 - - entrez-direct=16.2=he881be0_1 - - expat=2.4.8=h27087fc_0 - - fastqc=0.11.9=hdfd78af_1 - - font-ttf-dejavu-sans-mono=2.37=hab24e00_0 - - font-ttf-inconsolata=3.000=h77eed37_0 - - font-ttf-source-code-pro=2.038=h77eed37_0 - - font-ttf-ubuntu=0.83=hab24e00_0 - - fontconfig=2.14.0=hc2a2eb6_1 - - fonts-conda-ecosystem=1=0 - - fonts-conda-forge=1=0 - - fonttools=4.37.1=py38h0a891b7_0 - - fraggenescan=1.31=hec16e2b_4 - - freetype=2.12.1=hca18f0e_0 - - fribidi=1.0.10=h36c2ea0_0 - - future=0.18.2=py38h578d9bd_5 - - gcc_impl_linux-64=12.1.0=hea43390_16 - - gettext=0.19.8.1=h73d1719_1008 - - gfortran_impl_linux-64=12.1.0=h1db8e46_16 - - giflib=5.2.1=h36c2ea0_2 - - graphite2=1.3.13=h58526e2_1001 - - gsl=2.7=he838d99_0 - - gxx_impl_linux-64=12.1.0=hea43390_16 - - h5py=3.7.0=nompi_py38h045baee_101 - - harfbuzz=5.1.0=hf9f4e7c_0 - - hdf5=1.12.2=nompi_h2386368_100 - - hmmer=3.3.2=h87f3376_2 - - icu=70.1=h27087fc_0 - - idba=1.1.3=1 - - jpeg=9e=h166bdaf_2 - - kernel-headers_linux-64=2.6.32=he073ed8_15 - - keyutils=1.6.1=h166bdaf_0 - - kiwisolver=1.4.4=py38h43d8883_0 - - kraken-biom=1.2.0=pyh5e36f6f_0 - - kraken2=2.1.2=pl5321h9f5acd7_2 - - krb5=1.19.3=h3790be6_0 - - krona=2.8.1=pl5321hdfd78af_1 - - lcms2=2.12=hddcbb42_0 - - ld_impl_linux-64=2.36.1=hea4e1c9_2 - - lerc=3.0=h9c3ff4c_0 - - libblas=3.9.0=16_linux64_openblas - - libbrotlicommon=1.0.9=h166bdaf_7 - - libbrotlidec=1.0.9=h166bdaf_7 - - libbrotlienc=1.0.9=h166bdaf_7 - - libcblas=3.9.0=16_linux64_openblas - - libcups=2.3.3=h3e49a29_2 - - libcurl=7.83.1=h7bff187_0 - - libdeflate=1.10=h7f98852_0 - - libedit=3.1.20191231=he28a2e2_2 - - libev=4.33=h516909a_1 - - libffi=3.4.2=h7f98852_5 - - libgcc=7.2.0=h69d50b8_2 - - libgcc-devel_linux-64=12.1.0=h1ec3361_16 - - libgcc-ng=12.1.0=h8d9b700_16 - - libgfortran-ng=12.1.0=h69a702a_16 - - libgfortran5=12.1.0=hdcd56e2_16 - - libglib=2.72.1=h2d90d5f_0 - - libgomp=12.1.0=h8d9b700_16 - - libiconv=1.16=h516909a_0 - - libidn2=2.3.3=h166bdaf_0 - - liblapack=3.9.0=16_linux64_openblas - - libnghttp2=1.47.0=hdcd2b5c_1 - - libnsl=2.0.0=h7f98852_0 - - libopenblas=0.3.21=pthreads_h78a6416_3 - - libpng=1.6.37=h753d276_4 - - libsanitizer=12.1.0=ha89aaad_16 - - libsqlite=3.39.3=h753d276_0 - - libssh2=1.10.0=haa6b8db_3 - - libstdcxx-devel_linux-64=12.1.0=h1ec3361_16 - - libstdcxx-ng=12.1.0=ha89aaad_16 - - libtiff=4.4.0=h0fcbabc_0 - - libunistring=0.9.10=h7f98852_0 - - libuuid=2.32.1=h7f98852_1000 - - libwebp-base=1.2.4=h166bdaf_0 - - libxcb=1.13=h7f98852_1004 - - libxml2=2.9.14=h22db469_4 - - libzlib=1.2.12=h166bdaf_3 - - llvm-openmp=8.0.1=hc9558a2_0 - - lz4-c=1.9.3=h9c3ff4c_1 - - make=4.3=hd18ef5c_1 - - matplotlib-base=3.5.3=py38h38b5ce0_2 - - maxbin2=2.2.7=he1b5a44_1 - - munkres=1.1.4=pyh9f0ad1d_0 - - ncurses=6.3=h27087fc_1 - - numpy=1.23.3=py38h3a7f9d9_0 - - openjdk=17.0.3=h85293d2_2 - - openjpeg=2.5.0=h7d73246_1 - - openmp=8.0.1=0 - - openssl=1.1.1q=h166bdaf_0 - - packaging=21.3=pyhd8ed1ab_0 - - pandas=1.4.4=py38h47df419_0 - - pango=1.50.9=hc4f8a73_0 - - pcre=8.45=h9c3ff4c_0 - - pcre2=10.37=hc3806b6_1 - - perl=5.32.1=2_h7f98852_perl5 - - perl-archive-tar=2.40=pl5321hdfd78af_0 - - perl-base=2.23=pl5321hdfd78af_2 - - perl-business-isbn=3.007=pl5321hdfd78af_0 - - perl-business-isbn-data=20210112.006=pl5321hd8ed1ab_0 - - perl-carp=1.50=pl5321hd8ed1ab_0 - - perl-common-sense=3.75=pl5321hd8ed1ab_0 - - perl-compress-raw-bzip2=2.201=pl5321h166bdaf_0 - - perl-compress-raw-zlib=2.202=pl5321h166bdaf_0 - - perl-constant=1.33=pl5321hd8ed1ab_0 - - perl-data-dumper=2.183=pl5321h166bdaf_0 - - perl-digest-hmac=1.04=pl5321hdfd78af_0 - - perl-digest-md5=2.58=pl5321hec16e2b_1 - - perl-encode=3.19=pl5321hec16e2b_1 - - perl-encode-locale=1.05=pl5321hdfd78af_7 - - perl-exporter=5.74=pl5321hd8ed1ab_0 - - perl-exporter-tiny=1.002002=pl5321hd8ed1ab_0 - - perl-extutils-makemaker=7.64=pl5321hd8ed1ab_0 - - perl-file-listing=6.15=pl5321hdfd78af_0 - - perl-file-spec=3.48_01=pl5321hdfd78af_2 - - perl-html-parser=3.78=pl5321h9f5acd7_0 - - perl-html-tagset=3.20=pl5321hdfd78af_4 - - perl-http-cookies=6.10=pl5321hdfd78af_0 - - perl-http-daemon=6.14=pl5321hdfd78af_0 - - perl-http-date=6.05=pl5321hdfd78af_0 - - perl-http-message=6.36=pl5321hdfd78af_0 - - perl-http-negotiate=6.01=pl5321hdfd78af_4 - - perl-io-compress=2.201=pl5321h87f3376_0 - - perl-io-html=1.004=pl5321hdfd78af_0 - - perl-io-socket-ssl=2.075=pl5321hd8ed1ab_0 - - perl-io-zlib=1.11=pl5321hdfd78af_0 - - perl-json=4.09=pl5321hdfd78af_0 - - perl-json-xs=2.34=pl5321h9f5acd7_5 - - perl-libwww-perl=6.39=pl5321hdfd78af_1 - - perl-list-moreutils=0.430=pl5321hdfd78af_0 - - perl-list-moreutils-xs=0.430=pl5321hec16e2b_1 - - perl-lwp-mediatypes=6.04=pl5321hdfd78af_1 - - perl-lwp-simple=6.39=pl5321h9ee0642_5 - - perl-mime-base64=3.16=pl5321h166bdaf_0 - - perl-net-http=6.22=pl5321hdfd78af_0 - - perl-net-ssleay=1.92=pl5321haa6b8db_1 - - perl-ntlm=1.09=pl5321hdfd78af_5 - - perl-parent=0.238=pl5321hd8ed1ab_0 - - perl-pathtools=3.75=pl5321h166bdaf_0 - - perl-scalar-list-utils=1.63=pl5321h166bdaf_0 - - perl-socket=2.027=pl5321hec16e2b_3 - - perl-time-local=1.30=pl5321hdfd78af_0 - - perl-timedate=2.33=pl5321hdfd78af_2 - - perl-try-tiny=0.31=pl5321ha770c72_0 - - perl-types-serialiser=1.01=pl5321hdfd78af_0 - - perl-uri=5.12=pl5321hdfd78af_0 - - perl-url-encode=0.03=pl5321h9ee0642_0 - - perl-www-robotrules=6.02=pl5321hdfd78af_4 - - pillow=9.2.0=py38ha3b2c9c_2 - - pip=22.2.2=pyhd8ed1ab_0 - - pixman=0.40.0=h36c2ea0_0 - - popt=1.16=h0b475e3_2002 - - pplacer=1.1.alpha19=h9ee0642_2 - - prodigal=2.6.3=hec16e2b_4 - - pthread-stubs=0.4=h36c2ea0_1001 - - pyparsing=3.0.9=pyhd8ed1ab_0 - - pysam=0.19.1=py38h8bf8b8d_0 - - python=3.8.13=h582c2e5_0_cpython - - python-dateutil=2.8.2=pyhd8ed1ab_0 - - python_abi=3.8=2_cp38 - - pytz=2022.2.1=pyhd8ed1ab_0 - - r-base=4.1.3=ha8c3e7c_2 - - r-bitops=1.0_7=r41h06615bd_0 - - r-catools=1.18.2=r41h7525677_0 - - r-gplots=3.1.3=r41hc72bb7e_0 - - r-gtools=3.9.3=r41h06615bd_0 - - r-kernsmooth=2.23_20=r41h742201e_0 - - readline=8.1.2=h0f457ee_0 - - rsync=3.2.3=hfa40b15_4 - - scipy=1.9.1=py38hea3f02b_0 - - sed=4.8=he412f7d_0 - - setuptools=65.3.0=pyhd8ed1ab_1 - - six=1.16.0=pyh6c4a22f_0 - - spades=3.14.1=h95f258a_2 - - sqlite=3.39.3=h4ff8645_0 - - sysroot_linux-64=2.12=he073ed8_15 - - tar=1.34=ha1f6473_0 - - tk=8.6.12=h27826a3_0 - - tktable=2.10=hb7b940f_3 - - trimmomatic=0.39=hdfd78af_2 - - unicodedata2=14.0.0=py38h0a891b7_1 - - wget=1.20.3=ha56f1ee_1 - - wheel=0.37.1=pyhd8ed1ab_0 - - xorg-fixesproto=5.0=h7f98852_1002 - - xorg-inputproto=2.3.2=h7f98852_1002 - - xorg-kbproto=1.0.7=h7f98852_1002 - - xorg-libice=1.0.10=h7f98852_0 - - xorg-libsm=1.2.3=hd9c2040_1000 - - xorg-libx11=1.7.2=h7f98852_0 - - xorg-libxau=1.0.9=h7f98852_0 - - xorg-libxdmcp=1.1.3=h7f98852_0 - - xorg-libxext=1.3.4=h7f98852_1 - - xorg-libxfixes=5.0.3=h7f98852_1004 - - xorg-libxi=1.7.10=h7f98852_0 - - xorg-libxrender=0.9.10=h7f98852_1003 - - xorg-libxt=1.2.1=h7f98852_2 - - xorg-libxtst=1.2.3=h7f98852_1002 - - xorg-recordproto=1.14.2=h7f98852_1002 - - xorg-renderproto=0.11.1=h7f98852_1002 - - xorg-xextproto=7.3.0=h7f98852_1002 - - xorg-xproto=7.0.31=h7f98852_1007 - - xxhash=0.8.0=h7f98852_3 - - xz=5.2.6=h166bdaf_0 - - zlib=1.2.12=h166bdaf_3 - - zstd=1.5.2=h6239696_4 diff --git a/files/metagenomics-Ubuntu24.yml b/files/metagenomics-Ubuntu24.yml new file mode 100644 index 00000000..fd8820b0 --- /dev/null +++ b/files/metagenomics-Ubuntu24.yml @@ -0,0 +1,247 @@ +name: metagenomics +channels: + - defaults + - conda-forge + - bioconda +dependencies: + - _libgcc_mutex=0.1=main + - _openmp_mutex=5.1=1_gnu + - _r-mutex=1.0.1=anacondar_1 + - alsa-lib=1.2.14=hb9d3cd8_0 + - binutils_impl_linux-64=2.44=h4bf12b8_1 + - biom-format=2.1.17=py310h139afa4_0 + - blast=2.17.0=h66d330f_0 + - bowtie2=2.5.4=he96a11b_6 + - brotli=1.1.0=hb03c661_4 + - brotli-bin=1.1.0=hb03c661_4 + - bwidget=1.10.1=ha770c72_1 + - bzip2=1.0.8=h5eee18b_6 + - c-ares=1.34.5=hb9d3cd8_0 + - ca-certificates=2025.9.9=h06a4308_0 + - cached-property=1.5.2=hd8ed1ab_1 + - cached_property=1.5.2=pyha770c72_1 + - cairo=1.18.4=h3394656_0 + - checkm-genome=1.2.4=pyhdfd78af_2 + - click=8.2.1=pyh707e725_0 + - contourpy=1.3.2=py310h3788b33_0 + - curl=8.14.1=h332b0f4_0 + - cycler=0.12.1=pyhd8ed1ab_1 + - dendropy=5.0.8=pyhdfd78af_1 + - entrez-direct=24.0=he881be0_0 + - expat=2.7.1=h6a678d5_0 + - fastqc=0.12.1=hdfd78af_0 + - font-ttf-dejavu-sans-mono=2.37=hab24e00_0 + - font-ttf-inconsolata=3.000=h77eed37_0 + - font-ttf-source-code-pro=2.038=h77eed37_0 + - font-ttf-ubuntu=0.83=h77eed37_3 + - fontconfig=2.15.0=h7e30c49_1 + - fonts-conda-ecosystem=1=0 + - fonts-conda-forge=1=0 + - fonttools=4.59.2=py310h3406613_0 + - fraggenescan=1.32=h7b50bb2_0 + - freetype=2.14.0=ha770c72_1 + - fribidi=1.0.16=hb03c661_0 + - gcc_impl_linux-64=15.1.0=h4393ad2_5 + - gfortran_impl_linux-64=15.1.0=h3b9cdf2_5 + - giflib=5.2.2=hd590300_0 + - graphite2=1.3.14=hecca717_2 + - gsl=2.8=hbf7d49c_1 + - gxx_impl_linux-64=15.1.0=h6a1bac1_5 + - h5py=3.14.0=nompi_py310h4aa865e_101 + - harfbuzz=11.0.0=h76408a6_0 + - hdf5=1.14.6=nompi_h6e4c0c1_103 + - hmmer=3.4=h503566f_3 + - icu=75.1=he02047a_0 + - idba=1.1.3=pl5321h8ea774a_4 + - kernel-headers_linux-64=5.14.0=he073ed8_2 + - keyutils=1.6.3=hb9d3cd8_0 + - kiwisolver=1.4.9=py310haaf941d_1 + - kraken-biom=1.2.0=pyh5e36f6f_0 + - kraken2=2.1.6=pl5321h077b44d_0 + - krb5=1.21.3=h659f571_0 + - krona=2.8.1=pl5321hdfd78af_1 + - lcms2=2.17=h717163a_0 + - ld_impl_linux-64=2.44=h1423503_1 + - lerc=4.0.0=h0aef613_1 + - libaec=1.1.4=h3f801dc_0 + - libasprintf=0.25.1=h3f43e3d_1 + - libblas=3.9.0=35_h4a7cf45_openblas + - libbrotlicommon=1.1.0=hb03c661_4 + - libbrotlidec=1.1.0=hb03c661_4 + - libbrotlienc=1.1.0=hb03c661_4 + - libcblas=3.9.0=35_h0358290_openblas + - libcups=2.3.3=hb8b1518_5 + - libcurl=8.14.1=h332b0f4_0 + - libdeflate=1.22=hb9d3cd8_0 + - libedit=3.1.20250104=pl5321h7949ede_0 + - libev=4.33=hd590300_2 + - libexpat=2.7.1=hecca717_0 + - libffi=3.4.4=h6a678d5_1 + - libfreetype=2.14.0=ha770c72_1 + - libfreetype6=2.14.0=h73754d4_1 + - libgcc=15.1.0=h767d61c_5 + - libgcc-devel_linux-64=15.1.0=h4c094af_105 + - libgcc-ng=15.1.0=h69a702a_5 + - libgettextpo=0.25.1=h3f43e3d_1 + - libgfortran=15.1.0=h69a702a_5 + - libgfortran-ng=15.1.0=h69a702a_5 + - libgfortran5=15.1.0=hcea5267_5 + - libglib=2.84.0=h2ff4ddf_0 + - libgomp=15.1.0=h767d61c_5 + - libiconv=1.18=h3b78370_2 + - libidn2=2.3.8=ha4ef2c3_0 + - libjpeg-turbo=3.1.0=hb9d3cd8_0 + - liblapack=3.9.0=35_h47877c9_openblas + - libnghttp2=1.67.0=had1ee68_0 + - libnsl=2.0.1=hb9d3cd8_1 + - libopenblas=0.3.30=pthreads_h94d23a6_2 + - libpng=1.6.50=h421ea60_1 + - libsanitizer=15.1.0=h97b714f_5 + - libsqlite=3.50.4=h0c1763c_0 + - libssh2=1.11.1=hcf80075_0 + - libstdcxx=15.1.0=h8f9b012_5 + - libstdcxx-devel_linux-64=15.1.0=h4c094af_105 + - libstdcxx-ng=15.1.0=h4852527_5 + - libtiff=4.7.0=he137b08_1 + - libunistring=0.9.10=h7f98852_0 + - libuuid=2.41.1=he9a06e4_0 + - libwebp-base=1.6.0=hd42ef1d_0 + - libxcb=1.17.0=h9b100fa_0 + - libxcrypt=4.4.36=hd590300_1 + - libzlib=1.3.1=hb25bd0a_0 + - lz4-c=1.10.0=h5888daf_1 + - make=4.4.1=hb9d3cd8_2 + - matplotlib-base=3.10.6=py310hfde16b3_1 + - maxbin2=2.2.7=h503566f_7 + - mpi=1.0=openmpi + - munkres=1.1.4=pyhd8ed1ab_1 + - ncbi-vdb=3.2.1=h9948957_0 + - ncurses=6.5=h7934f7d_0 + - numpy=2.2.6=py310hefbff90_0 + - openjdk=23.0.2=h53dfc1b_2 + - openjpeg=2.5.3=h55fea9a_1 + - openmpi=4.1.6=hc5af2df_101 + - openssl=3.5.2=h26f9b46_0 + - packaging=25.0=pyh29332c3_1 + - pandas=2.3.2=py310h0158d43_0 + - pango=1.56.3=h9ac818e_1 + - pcre2=10.44=hc749103_2 + - perl=5.32.1=7_hd590300_perl5 + - perl-archive-tar=3.04=pl5321hdfd78af_0 + - perl-b-cow=0.007=pl5321hb9d3cd8_1 + - perl-base=2.23=pl5321hd8ed1ab_0 + - perl-business-isbn=3.007=pl5321hd8ed1ab_0 + - perl-business-isbn-data=20210112.006=pl5321hd8ed1ab_0 + - perl-carp=1.50=pl5321hd8ed1ab_0 + - perl-clone=0.46=pl5321hb9d3cd8_1 + - perl-common-sense=3.75=pl5321hd8ed1ab_0 + - perl-compress-raw-bzip2=2.213=pl5321hda65f42_0 + - perl-compress-raw-zlib=2.213=pl5321h4dac143_0 + - perl-constant=1.33=pl5321hd8ed1ab_0 + - perl-data-dump=1.25=pl5321h7b50bb2_2 + - perl-digest-hmac=1.05=pl5321hdfd78af_0 + - perl-digest-md5=2.59=pl5321hb9d3cd8_3 + - perl-encode=3.21=pl5321hb9d3cd8_1 + - perl-encode-locale=1.05=pl5321hdfd78af_7 + - perl-exporter=5.74=pl5321hd8ed1ab_0 + - perl-exporter-tiny=1.002002=pl5321hd8ed1ab_0 + - perl-extutils-makemaker=7.70=pl5321hd8ed1ab_0 + - perl-file-listing=6.16=pl5321hdfd78af_0 + - perl-file-spec=3.48_01=pl5321hdfd78af_2 + - perl-html-parser=3.81=pl5321h4ac6f70_1 + - perl-html-tagset=3.24=pl5321hdfd78af_0 + - perl-http-cookiejar-lwp=0.014=pl5321hdfd78af_0 + - perl-http-cookies=6.11=pl5321hdfd78af_0 + - perl-http-daemon=6.16=pl5321hdfd78af_0 + - perl-http-date=6.06=pl5321hdfd78af_0 + - perl-http-message=7.00=pl5321hdfd78af_0 + - perl-http-negotiate=6.01=pl5321hdfd78af_4 + - perl-io-compress=2.213=pl5321h503566f_0 + - perl-io-html=1.004=pl5321hdfd78af_0 + - perl-io-socket-ssl=2.075=pl5321hd8ed1ab_0 + - perl-io-zlib=1.15=pl5321hdfd78af_1 + - perl-json=4.10=pl5321hdfd78af_1 + - perl-json-xs=4.04=pl5321h9948957_0 + - perl-libwww-perl=6.80=pl5321hdfd78af_0 + - perl-list-moreutils=0.430=pl5321hdfd78af_0 + - perl-list-moreutils-xs=0.430=pl5321h7b50bb2_5 + - perl-lwp-mediatypes=6.04=pl5321hdfd78af_1 + - perl-lwp-protocol-https=6.14=pl5321hdfd78af_1 + - perl-mime-base64=3.16=pl5321hb9d3cd8_3 + - perl-module-load=0.34=pl5321hdfd78af_0 + - perl-mozilla-ca=20250602=pl5321hdfd78af_0 + - perl-net-http=6.24=pl5321hdfd78af_0 + - perl-net-ssleay=1.94=pl5321hf672d98_1 + - perl-ntlm=1.09=pl5321hdfd78af_5 + - perl-parent=0.243=pl5321hd8ed1ab_0 + - perl-pathtools=3.75=pl5321hb9d3cd8_2 + - perl-scalar-list-utils=1.70=pl5321hb03c661_0 + - perl-socket=2.027=pl5321h5c03b87_6 + - perl-storable=3.15=pl5321hb9d3cd8_2 + - perl-test-fatal=0.016=pl5321ha770c72_0 + - perl-test-needs=0.002009=pl5321hd8ed1ab_0 + - perl-test-requiresinternet=0.05=pl5321hdfd78af_1 + - perl-test-warnings=0.031=pl5321ha770c72_0 + - perl-time-local=1.35=pl5321hdfd78af_0 + - perl-timedate=2.33=pl5321hdfd78af_2 + - perl-try-tiny=0.31=pl5321ha770c72_0 + - perl-types-serialiser=1.01=pl5321hdfd78af_0 + - perl-uri=5.32=pl5321ha770c72_1 + - perl-url-encode=0.03=pl5321h9ee0642_1 + - perl-www-robotrules=6.02=pl5321hdfd78af_4 + - pillow=11.3.0=py310hb7da693_1 + - pip=25.2=pyhc872135_0 + - pixman=0.46.4=h54a6638_1 + - popt=1.16=h0b475e3_2002 + - pplacer=1.1.alpha20=hd563303_0 + - prodigal=2.6.3=h577a1d6_11 + - pthread-stubs=0.3=h0ce48e5_1 + - pyparsing=3.2.4=pyhcf101f3_0 + - pysam=0.22.1=py310h804392c_2 + - python=3.10.15=h4a871b0_2_cpython + - python-dateutil=2.9.0.post0=pyhe01879c_2 + - python-tzdata=2025.2=pyhd8ed1ab_0 + - python_abi=3.10=8_cp310 + - pytz=2025.2=pyhd8ed1ab_0 + - qhull=2020.2=h434a139_5 + - r-base=4.2.3=hc0fa579_17 + - r-bitops=1.0_7=r42h57805ef_2 + - r-catools=1.18.2=r42ha503ecb_2 + - r-gplots=3.1.3.1=r42hc72bb7e_0 + - r-gtools=3.9.5=r42h57805ef_0 + - r-kernsmooth=2.23_24=r42hc2011d3_0 + - readline=8.3=hc2a1206_0 + - rsync=3.4.1=h81c0278_2 + - scipy=1.15.2=py310h1d65ade_0 + - sed=4.9=h6688a6e_0 + - setuptools=78.1.1=py310h06a4308_0 + - six=1.17.0=pyhe01879c_1 + - spades=4.2.0=h8d6e82b_1 + - sqlite=3.50.2=hb25bd0a_1 + - sysroot_linux-64=2.34=h087de78_2 + - tar=1.35=h3b78370_0 + - tk=8.6.15=h54e0aa7_0 + - tktable=2.10=h8d826fa_7 + - trimmomatic=0.40=hdfd78af_0 + - tzdata=2025b=h04d1e81_0 + - unicodedata2=16.0.0=py310h7c4b9e2_1 + - wget=1.21.4=hda4d442_0 + - wheel=0.45.1=py310h06a4308_0 + - xorg-libice=1.1.2=hb9d3cd8_0 + - xorg-libsm=1.2.6=he73a12e_0 + - xorg-libx11=1.8.12=h9b100fa_1 + - xorg-libxau=1.0.12=h9b100fa_0 + - xorg-libxdmcp=1.1.5=h9b100fa_0 + - xorg-libxext=1.3.6=hb9d3cd8_0 + - xorg-libxfixes=6.0.1=hb9d3cd8_0 + - xorg-libxi=1.8.2=hb9d3cd8_0 + - xorg-libxrandr=1.5.4=hb9d3cd8_0 + - xorg-libxrender=0.9.12=hb9d3cd8_0 + - xorg-libxt=1.3.1=hb9d3cd8_0 + - xorg-libxtst=1.2.5=hb9d3cd8_3 + - xorg-xorgproto=2024.1=h5eee18b_1 + - xxhash=0.8.3=hb47aa4a_0 + - xz=5.6.4=h5eee18b_1 + - zlib=1.3.1=hb25bd0a_0 + - zstd=1.5.7=hb8e6e7a_2 +prefix: /home/dcuser/miniconda3/envs/metagenomics diff --git a/files/spec-file-Ubuntu22.txt b/files/spec-file-Ubuntu22.txt deleted file mode 100644 index 89e59e94..00000000 --- a/files/spec-file-Ubuntu22.txt +++ /dev/null @@ -1,231 +0,0 @@ -# This file may be used to create an environment using: -# $ conda create --name --file -# platform: linux-64 -@EXPLICIT -https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h5bd9786_13.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 -https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.6.15.2-ha878542_0.tar.bz2 -https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2 -https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2 -https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2 -https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-hab24e00_0.tar.bz2 -https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-2.6.32-he073ed8_15.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.36.1-hea4e1c9_2.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libgcc-devel_linux-64-12.1.0-h1ec3361_16.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-12.1.0-hdcd56e2_16.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-devel_linux-64-12.1.0-h1ec3361_16.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-12.1.0-ha89aaad_16.tar.bz2 -https://conda.anaconda.org/bioconda/linux-64/pplacer-1.1.alpha19-h9ee0642_2.tar.bz2 -https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-12.1.0-h69a702a_16.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-12.1.0-h8d9b700_16.tar.bz2 -https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.12-he073ed8_15.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.36.1-h193b22a_2.tar.bz2 -https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.1.0-h8d9b700_16.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.7.2-h166bdaf_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.18.1-h7f98852_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/expat-2.4.8-h27087fc_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.10-h36c2ea0_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.1-h36c2ea0_2.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h58526e2_1001.tar.bz2 -https://conda.anaconda.org/bioconda/linux-64/hmmer-3.3.2-h87f3376_2.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/icu-70.1-h27087fc_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/jpeg-9e-h166bdaf_2.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/lerc-3.0-h9c3ff4c_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libbrotlicommon-1.0.9-h166bdaf_7.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.10-h7f98852_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h516909a_1.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libgcc-7.2.0-h69d50b8_2.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.16-h516909a_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.21-pthreads_h78a6416_3.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libsanitizer-12.1.0-ha89aaad_16.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libunistring-0.9.10-h7f98852_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.32.1-h7f98852_1000.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.2.4-h166bdaf_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.12-h166bdaf_3.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/llvm-openmp-8.0.1-hc9558a2_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.3-h9c3ff4c_1.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/make-4.3-hd18ef5c_1.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.3-h27087fc_1.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/openssl-1.1.1q-h166bdaf_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/pcre-8.45-h9c3ff4c_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/pixman-0.40.0-h36c2ea0_0.tar.bz2 -https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.3-hec16e2b_4.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/sed-4.8-he412f7d_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/xorg-inputproto-2.3.2-h7f98852_1002.tar.bz2 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