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U54Bioinformatics / PhylinSic_Project

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Package versions? #2

Closed gitUser128954 closed 1 year ago

gitUser128954 commented 1 year ago

I know you had rJava and picard/gatk4 issues, but can you provide the package version numbers for the working conda environment?

jefftc commented 1 year ago

Below is a list of the packages installed in my conda environment.

As you noted, I had issues with some of the libraries in conda (rJava, gatk4). I worked around it by installing those packages separately, and ran the non-conda versions by configuring the following variables in the Snakefile: GATK RSCRIPT JAVA BEAST2_DIR LOGCOMBINER

Good luck! I wish the installation were easier. Hopefully, the issues will eventually resolve themselves when the conda packages are updated, or someone who is better at conda than me has a better solution.

Jeff

packages in environment at /home/jchang4/mambaforge/envs/snakemake:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge _r-mutex 1.0.1 anacondar_1 conda-forge aioeasywebdav 2.4.0 pyha770c72_0 conda-forge aiohttp 3.8.5 py311h459d7ec_0 conda-forge aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge alsa-lib 1.2.9 hd590300_0 conda-forge amply 0.1.6 pyhd8ed1ab_0 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge astroid 2.15.5 pypi_0 pypi async-timeout 4.0.2 pyhd8ed1ab_0 conda-forge attmap 0.13.2 pyhd8ed1ab_0 conda-forge attrs 23.1.0 pyh71513ae_1 conda-forge backports 1.0 pyhd8ed1ab_3 conda-forge backports.functools_lru_cache 1.6.5 pyhd8ed1ab_0 conda-forge bcrypt 3.2.2 py311hd4cff14_1 conda-forge binutils_impl_linux-64 2.40 hf600244_0 conda-forge bioconductor-ggtree 3.6.0 r42hdfd78af_0 bioconda bioconductor-treeio 1.22.0 r42hdfd78af_0 bioconda boltons 23.0.0 pyhd8ed1ab_0 conda-forge boto3 1.28.9 pyhd8ed1ab_0 conda-forge botocore 1.31.9 pyhd8ed1ab_0 conda-forge brotlipy 0.7.0 py311hd4cff14_1005 conda-forge bwidget 1.9.14 ha770c72_1 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.19.1 hd590300_0 conda-forge ca-certificates 2023.7.22 hbcca054_0 conda-forge cachetools 5.3.1 pyhd8ed1ab_0 conda-forge cairo 1.16.0 hbbf8b49_1016 conda-forge certifi 2023.7.22 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py311h409f033_3 conda-forge charset-normalizer 3.2.0 pyhd8ed1ab_0 conda-forge coin-or-cbc 2.10.10 h9002f0b_0 conda-forge coin-or-cgl 0.60.7 h516709c_0 conda-forge coin-or-clp 1.17.8 h1ee7a9c_0 conda-forge coin-or-osi 0.108.8 ha2443b9_0 conda-forge coin-or-utils 2.11.9 hee58242_0 conda-forge coincbc 2.10.10 0_metapackage conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge conda 23.3.1 py311h38be061_0 conda-forge conda-package-handling 2.0.2 pyh38be061_0 conda-forge conda-package-streaming 0.8.0 pyhd8ed1ab_0 conda-forge configargparse 1.5.5 pyhd8ed1ab_0 conda-forge connection_pool 0.0.3 pyhd3deb0d_0 conda-forge cryptography 41.0.2 py311h63ff55d_0 conda-forge curl 8.2.0 hca28451_0 conda-forge datrie 0.8.2 py311hd4cff14_6 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge dill 0.3.6 pypi_0 pypi docutils 0.20.1 py311h38be061_0 conda-forge dpath 2.1.6 pyha770c72_0 conda-forge dropbox 11.36.2 pyhd8ed1ab_0 conda-forge exceptiongroup 1.1.2 pyhd8ed1ab_0 conda-forge expat 2.5.0 hcb278e6_1 conda-forge filechunkio 1.8 py_2 conda-forge filelock 3.12.2 pyhd8ed1ab_0 conda-forge fmt 9.1.0 h924138e_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 hab24e00_0 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge freetype 2.12.1 hca18f0e_1 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge frozenlist 1.4.0 py311h459d7ec_0 conda-forge ftputil 5.0.4 pyhd8ed1ab_0 conda-forge gcc_impl_linux-64 13.1.0 hc4be1a9_0 conda-forge gettext 0.21.1 h27087fc_0 conda-forge gfortran_impl_linux-64 13.1.0 hd511a9b_0 conda-forge giflib 5.2.1 h0b41bf4_3 conda-forge gitdb 4.0.10 pyhd8ed1ab_0 conda-forge gitpython 3.1.32 pyhd8ed1ab_0 conda-forge glpk 5.0 h445213a_0 conda-forge gmp 6.2.1 h58526e2_0 conda-forge google-api-core 2.11.1 pyhd8ed1ab_0 conda-forge google-api-python-client 2.94.0 pyhd8ed1ab_0 conda-forge google-auth 2.22.0 pyh1a96a4e_0 conda-forge google-auth-httplib2 0.1.0 pyhd8ed1ab_1 conda-forge google-cloud-core 2.3.3 pyhd8ed1ab_0 conda-forge google-cloud-storage 2.10.0 pyh1a96a4e_0 conda-forge google-crc32c 1.1.2 py311h98db957_4 conda-forge google-resumable-media 2.5.0 pyhd8ed1ab_0 conda-forge googleapis-common-protos 1.59.1 pyhd8ed1ab_0 conda-forge graphite2 1.3.13 h58526e2_1001 conda-forge grpcio 1.56.2 py311ha6695c7_0 conda-forge gsl 2.7 he838d99_0 conda-forge gxx_impl_linux-64 13.1.0 hc4be1a9_0 conda-forge harfbuzz 7.3.0 hdb3a94d_0 conda-forge htslib 1.17 h81da01d_2 bioconda httplib2 0.22.0 pyhd8ed1ab_0 conda-forge humanfriendly 10.0 py311h38be061_4 conda-forge icu 72.1 hcb278e6_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge importlib_resources 6.0.0 pyhd8ed1ab_1 conda-forge iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge isort 5.12.0 pypi_0 pypi jinja2 3.1.2 pyhd8ed1ab_1 conda-forge jmespath 1.0.1 pyhd8ed1ab_0 conda-forge jsonpatch 1.32 pyhd8ed1ab_0 conda-forge jsonpointer 2.0 py_0 conda-forge jsonschema 4.18.4 pyhd8ed1ab_0 conda-forge jsonschema-specifications 2023.7.1 pyhd8ed1ab_0 conda-forge jupyter_core 5.3.1 py311h38be061_0 conda-forge kernel-headers_linux-64 2.6.32 he073ed8_16 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge krb5 1.21.1 h659d440_0 conda-forge lazy-object-proxy 1.9.0 pypi_0 pypi lcms2 2.15 haa2dc70_1 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libabseil 20230125.3 cxx17_h59595ed_0 conda-forge libarchive 3.6.2 h039dbb9_1 conda-forge libblas 3.9.0 17_linux64_openblas conda-forge libcblas 3.9.0 17_linux64_openblas conda-forge libcrc32c 1.1.2 h9c3ff4c_0 conda-forge libcups 2.3.3 h4637d8d_4 conda-forge 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4.23.3 hd1fb520_0 conda-forge libsanitizer 13.1.0 hfd8a6a1_0 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libsolv 0.7.24 hfc55251_1 conda-forge libsqlite 3.42.0 h2797004_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-devel_linux-64 13.1.0 he3cc6c4_0 conda-forge libstdcxx-ng 13.1.0 hfd8a6a1_0 conda-forge libtiff 4.5.1 h8b53f26_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libwebp-base 1.3.1 hd590300_0 conda-forge libxcb 1.15 h0b41bf4_0 conda-forge libxml2 2.11.4 h0d562d8_0 conda-forge libzlib 1.2.13 hd590300_5 conda-forge logmuse 0.2.6 pyh8c360ce_0 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge lzo 2.10 h516909a_1000 conda-forge make 4.3 hd18ef5c_1 conda-forge mamba 1.4.9 py311h3072747_0 conda-forge markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge markupsafe 2.1.3 py311h459d7ec_0 conda-forge mccabe 0.7.0 pypi_0 pypi mdurl 0.1.0 pyhd8ed1ab_0 conda-forge multidict 6.0.4 py311h2582759_0 conda-forge nbformat 5.9.1 pyhd8ed1ab_0 conda-forge ncurses 6.4 hcb278e6_0 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conda-forge pyasn1-modules 0.2.7 py_0 conda-forge pybind11-abi 4 hd8ed1ab_3 conda-forge pycosat 0.6.4 py311hd4cff14_1 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pygments 2.15.1 pyhd8ed1ab_0 conda-forge pylint 2.17.4 pypi_0 pypi pynacl 1.5.0 py311hd4cff14_2 conda-forge pyopenssl 23.2.0 pyhd8ed1ab_1 conda-forge pyparsing 3.1.0 pyhd8ed1ab_0 conda-forge pysftp 0.2.9 py_1 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge pytest 7.4.0 pyhd8ed1ab_0 conda-forge python 3.11.4 hab00c5b_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-fastjsonschema 2.17.1 pyhd8ed1ab_0 conda-forge python-irodsclient 1.1.8 pyhd8ed1ab_0 conda-forge python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge python_abi 3.11 3_cp311 conda-forge pytz 2023.3 pyhd8ed1ab_0 conda-forge pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge pyyaml 6.0 py311hd4cff14_5 conda-forge r-ape 5.7_1 r42h08d816e_1 conda-forge r-aplot 0.1.10 r42hc72bb7e_1 conda-forge r-askpass 1.1 r42h57805ef_4 conda-forge r-assertthat 0.2.1 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r-patchwork 1.1.2 r42hc72bb7e_2 conda-forge r-phangorn 2.11.1 r42h7ce84a7_1 conda-forge r-pillar 1.9.0 r42hc72bb7e_1 conda-forge r-pkgbuild 1.4.2 r42hc72bb7e_0 conda-forge r-pkgconfig 2.0.3 r42hc72bb7e_3 conda-forge r-pkgdown 2.0.7 r42hc72bb7e_1 conda-forge r-pkgload 1.3.2.1 r42hc72bb7e_0 conda-forge r-plottools 0.2.0 r42hc72bb7e_1 conda-forge r-praise 1.0.0 r42hc72bb7e_1007 conda-forge r-prettyunits 1.1.1 r42hc72bb7e_3 conda-forge r-processx 3.8.2 r42h57805ef_0 conda-forge r-profvis 0.3.8 r42h57805ef_2 conda-forge r-promises 1.2.0.1 r42ha503ecb_2 conda-forge r-ps 1.7.5 r42h57805ef_1 conda-forge r-purrr 1.0.1 r42h57805ef_1 conda-forge r-quadprog 1.5_8 r42h13b3f57_5 conda-forge r-r.cache 0.16.0 r42hc72bb7e_2 conda-forge r-r.methodss3 1.8.2 r42hc72bb7e_2 conda-forge r-r.oo 1.25.0 r42hc72bb7e_2 conda-forge r-r.utils 2.12.2 r42hc72bb7e_1 conda-forge r-r6 2.5.1 r42hc72bb7e_2 conda-forge r-ragg 1.2.5 r42h85cdef0_2 conda-forge r-rappdirs 0.3.3 r42h57805ef_2 conda-forge r-rbibutils 2.2.13 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On Oct 19, 2023, at 9:26 AM, gitUser128954 @.***> wrote:

I know you had rJava and picard/gatk4 issues, but can you provide the package version numbers for the working conda environment? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>

gitUser128954 commented 1 year ago

Thank you! I hope it works without an issue too, but just in case.