search

franciscozorrilla / metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
https://franciscozorrilla.github.io/metaGEM/
MIT License
203 stars 42 forks source link

[Question]: Install on mac M2? #134

Closed transition-bio-1 closed 11 months ago

transition-bio-1 commented 1 year ago

Hi Francisco,

I'm relatively inexperienced in bioinformatics and maybe there is an easy workaround that I'm missing, but I am struggling to figure out if this workflow can be run on a mac M2 machine. At the very least concoct v1.1.0 is not available for osx-64 (only 0.4.2) and I'm not sure about other dependencies. Do you have any suggestions for how to set up metaGEM on a mac? The workflow itself looks excellent and I would love to try it out.

Best, ~s.

franciscozorrilla commented 1 year ago

Hi Sasha,

Great that you are getting hands on experience with bioinfo tools, happy to help!

The short answer is: no ❌

The long answer is: metaGEM was developed for usage on linux-based high performance computer clusters, considering that personal computers (mac or windows) do not have the computational resources to efficiently store and analyze real metagenomics datasets. Even if you could set up metaGEM on your macbook, you would have a very hard time with many steps in the workflow, e.g. short read assembly which typically requires multiple cores and significant RAM. So while it should be possible to install dependencies and set up metaGEM on a macbook, this would be of very limited use. Instead, I would suggest you get access to your institution's high performance computer cluster, where you should be able to set up metaGEM ✅

See also issues #16 and #122 for more info on this topic. You may also be interested in this google colab notebook that sets up metaGEM and runs assembly on a toy set of samples.

Best wishes and good luck! Francisco

transition-bio-1 commented 1 year ago

Thanks for a quick response!

I figured that was probably going to be the answer. The M2 machines are actually getting up there in cores and RAM availability for smaller jobs. I have a somewhat unique use case with small enough datasets that I was hoping to crunch at a leisurely pace :)

Still. A great workflow and pretty instructive. Thank you!

Sasha Milshteyn, PhD Founder, Transition Bio[mining] Tel: +1.415.680.3435

On Thu, Jul 20, 2023 at 4:05 AM Francisco Zorrilla @.***> wrote:

Hi Sasha,

Great that you are getting hands on experience with bioinfo tools, happy to help!

The short answer is: no ❌

The long answer is: metaGEM was developed for usage on linux-based high performance computer clusters, considering that personal computers (mac or windows) do not have the computational resources to efficiently store and analyze real metagenomics datasets. Even if you could set up metaGEM on your macbook, you would have a very hard time with many steps in the workflow, e.g. short read assembly which typically requires multiple cores and significant RAM. So while it should be possible to install dependencies and set up metaGEM on a macbook, this would be of very limited use. Instead, I would suggest you get access to your institution's high performance computer cluster, where you should be able to set up metaGEM ✅

See also issues #16 https://github.com/franciscozorrilla/metaGEM/issues/16 and #122 https://github.com/franciscozorrilla/metaGEM/issues/122 for more info on this topic. You may also be interested in this google colab notebook https://colab.research.google.com/drive/1I1S8AoGuJ9Oc2292vqAGTDmZcbnolbuj#scrollTo=awiAaVwSF5Fz that sets up metaGEM and runs assembly on a toy set of samples.

Best wishes and good luck! Francisco

— Reply to this email directly, view it on GitHub https://github.com/franciscozorrilla/metaGEM/issues/134#issuecomment-1643722154, or unsubscribe https://github.com/notifications/unsubscribe-auth/BBGWNMOGX6VQOUIX42AF7JLXREGGFANCNFSM6AAAAAA2QP6GTE . You are receiving this because you authored the thread.Message ID: @.***>

franciscozorrilla commented 1 year ago

Its true, I also think that for certain tasks/datasets there could be situations where it would be nice to run some analysis with metaGEM on a macbook (#123). Its not at the top of my priority list but will try to get to this soon 💎

franciscozorrilla commented 1 year ago

Was curious about this so looked into it earlier than expected.

There is good news and bad news: as a temporary workaround you can follow the instructions from the manual setup to install dependencies from yml files.

Unfortunately, gtdbtk is not available on osx due to the fact that a key dependency pplacer is only available for linux architectures. In any case, gtdbtk is far too computationally intensive to run on a macbook, even with M1/M2. Also, as you already identified CONCOCT v1.1.0 is not avaiable for osx so you would have to settle for the earlier v0.4.2 for now.

First create a modified version of the metaGEM_env.yml file, with relaxed versioning for CONCOCT and gtdbtk removed:

name: metagem
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - bedtools>=2.29.2
  - bwa>=0.7.17
  - concoct
  - diamond>=2.0.6
  - fastp>=0.20.1
  - maxbin2>=2.2.7
  - megahit>=1.2.9
  - metabat2>=2.15
  - r-base>=3.5.1
  - r-gridextra>=2.2.1
  - r-tidyverse
  - r-tidytext
  - samtools>=1.9
  - snakemake>=5.10.0,<5.31.1

Then use mamba to set up the dependencies:

$ mamba env create --prefix ./envs/metagem -f metaGEM_env.yml
``` pkgs/main/osx-64 [====================] (00m:00s) No change bioconda/osx-64 [====================] (00m:00s) No change pkgs/r/noarch [====================] (00m:00s) No change bioconda/noarch [====================] (00m:00s) No change pkgs/r/osx-64 [====================] (00m:00s) No change pkgs/main/noarch [====================] (00m:00s) No change conda-forge/noarch [====================] (00m:03s) Done conda-forge/osx-64 [====================] (00m:08s) Done Looking for: ["bedtools[version='>=2.29.2']", "bwa[version='>=0.7.17']", 'concoct', "diamond[version='>=2.0.6']", "fastp[version='>=0.20.1']", "maxbin2[version='>=2.2.7']", "megahit[version='>=1.2.9']", "metabat2[version='>=2.15']", "r-base[version='>=3.5.1']", "r-gridextra[version='>=2.2.1']", 'r-tidyverse', 'r-tidytext', "samtools[version='>=1.9']", "snakemake[version='>=5.10.0,<5.31.1']"] Transaction Prefix: /Users/fzorrilla/Documents/metagem/envs/metagem Updating specs: - bedtools[version='>=2.29.2'] - bwa[version='>=0.7.17'] - concoct - diamond[version='>=2.0.6'] - fastp[version='>=0.20.1'] - maxbin2[version='>=2.2.7'] - megahit[version='>=1.2.9'] - metabat2[version='>=2.15'] - r-base[version='>=3.5.1'] - r-gridextra[version='>=2.2.1'] - r-tidyverse - r-tidytext - samtools[version='>=1.9'] - snakemake[version='>=5.10.0,<5.31.1'] Package Version Build Channel Size ────────────────────────────────────────────────────────────────────────────────────────────────────────── Install: ────────────────────────────────────────────────────────────────────────────────────────────────────────── + _r-mutex 1.0.1 anacondar_1 conda-forge/noarch Cached + aioeasywebdav 2.4.0 py36h79c6626_1001 conda-forge/osx-64 Cached + aiohttp 3.7.4.post0 py36hfa26744_0 conda-forge/osx-64 Cached + alabaster 0.7.13 pyhd8ed1ab_0 conda-forge/noarch 18 KB + amply 0.1.6 pyhd8ed1ab_0 conda-forge/noarch 21 KB + appdirs 1.4.4 pyh9f0ad1d_0 conda-forge/noarch Cached + async-timeout 3.0.1 py_1000 conda-forge/noarch Cached + attrs 22.2.0 pyh71513ae_0 conda-forge/noarch 53 KB + babel 2.11.0 pyhd8ed1ab_0 conda-forge/noarch 7 MB + backports 1.0 pyhd8ed1ab_3 conda-forge/noarch 6 KB + backports.functools_lru_cache 1.6.5 pyhd8ed1ab_0 conda-forge/noarch 11 KB + bcrypt 3.2.0 py36hfa26744_1 conda-forge/osx-64 Cached + bedtools 2.31.0 h6372da2_2 bioconda/osx-64 768 KB + biopython 1.79 py36hfa26744_0 conda-forge/osx-64 Cached + blas 1.1 openblas conda-forge/osx-64 Cached + blast 2.14.0 pl5321h91c44f7_2 bioconda/osx-64 232 MB + boto3 1.21.32 pyhd8ed1ab_0 conda-forge/noarch 71 KB + botocore 1.24.32 pyhd3eb1b0_0 pkgs/main/noarch 4 MB + bowtie2 2.5.1 py36hde6f128_1 bioconda/osx-64 1 MB + brotlipy 0.7.0 py36hfa26744_1001 conda-forge/osx-64 Cached + bwa 0.7.17 h45fc8d7_11 bioconda/osx-64 222 KB + bwidget 1.9.14 h694c41f_1 conda-forge/osx-64 Cached + bzip2 1.0.8 h0d85af4_4 conda-forge/osx-64 Cached + c-ares 1.19.1 h0dc2134_0 conda-forge/osx-64 101 KB + ca-certificates 2023.5.7 h8857fd0_0 conda-forge/osx-64 145 KB + cachetools 5.0.0 pyhd8ed1ab_0 conda-forge/noarch 12 KB + cairo 1.16.0 h0ab9d94_1001 conda-forge/osx-64 1 MB + cctools_osx-64 973.0.1 hcc6d90d_13 conda-forge/osx-64 1 MB + certifi 2021.5.30 py36h79c6626_0 conda-forge/osx-64 Cached + cffi 1.14.4 py36h1b827b8_0 conda-forge/osx-64 Cached + chardet 4.0.0 py36h79c6626_1 conda-forge/osx-64 Cached + charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge/noarch 36 KB + clang 14.0.6 h694c41f_1 conda-forge/osx-64 130 KB + clang-14 14.0.6 default_hdb78580_1 conda-forge/osx-64 1005 KB + clang_osx-64 14.0.6 h3113cd8_6 conda-forge/osx-64 20 KB + clangxx 14.0.6 default_hdb78580_1 conda-forge/osx-64 130 KB + clangxx_osx-64 14.0.6 h6f97653_6 conda-forge/osx-64 19 KB + coincbc 2.10.3 h7a5a08d_3 conda-forge/osx-64 Cached + colorama 0.4.5 pyhd8ed1ab_0 conda-forge/noarch 18 KB + compiler-rt 14.0.6 h613da45_0 conda-forge/osx-64 83 KB + compiler-rt_osx-64 14.0.6 hab78ec2_0 conda-forge/noarch 15 MB + concoct 0.4.1 py36hd1ccf6d_0 bioconda/osx-64 Cached + configargparse 1.5.5 pyhd8ed1ab_0 conda-forge/noarch 40 KB + cryptography 35.0.0 py36ha6a00b0_0 conda-forge/osx-64 Cached + curl 7.68.0 h8754def_0 conda-forge/osx-64 Cached + cycler 0.11.0 pyhd8ed1ab_0 conda-forge/noarch Cached + cython 0.29.24 py36hefe7e0e_0 conda-forge/osx-64 Cached + datrie 0.8.2 py36hfa26744_2 conda-forge/osx-64 Cached + decorator 5.1.1 pyhd8ed1ab_0 conda-forge/noarch 12 KB + defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge/noarch 23 KB + diamond 2.1.8 h94ec1f5_0 bioconda/osx-64 3 MB + docutils 0.17.1 py36h79c6626_0 conda-forge/osx-64 Cached + dropbox 11.36.2 pyhd8ed1ab_0 conda-forge/noarch 956 KB + entrez-direct 16.2 h193322a_1 bioconda/osx-64 7 MB + fastp 0.23.4 h5712c04_2 bioconda/osx-64 237 KB + fftw 3.3.8 mpi_mpich_h6e18f22_1009 conda-forge/osx-64 5 MB + filechunkio 1.8 py_2 conda-forge/noarch Cached + fontconfig 2.13.1 h1027ab8_1000 conda-forge/osx-64 Cached + fraggenescan 1.31 h2413b67_6 bioconda/osx-64 1 MB + freetype 2.12.1 h3f81eb7_1 conda-forge/osx-64 586 KB + ftputil 5.0.4 pyhd8ed1ab_0 conda-forge/noarch 42 KB + gdk-pixbuf 2.36.12 h306395f_1005 conda-forge/osx-64 565 KB + gettext 0.21.1 h8a4c099_0 conda-forge/osx-64 4 MB + gfortran_osx-64 4.8.5 h22b1bf0_8 conda-forge/osx-64 Cached + ghostscript 9.54.0 h96cf925_2 conda-forge/osx-64 56 MB + giflib 5.1.7 h01d97ff_1 conda-forge/osx-64 Cached + gitdb 4.0.10 pyhd8ed1ab_0 conda-forge/noarch 50 KB + gitpython 3.1.18 pyhd8ed1ab_0 conda-forge/noarch Cached + glib 2.66.3 h519c658_0 conda-forge/osx-64 491 KB + gobject-introspection 1.66.1 py36h251bb5a_3 conda-forge/osx-64 1 MB + google-api-core 2.8.0 pyhd8ed1ab_1 conda-forge/noarch 70 KB + google-api-python-client 2.52.0 pyhd8ed1ab_0 conda-forge/noarch 5 MB + google-auth 2.22.0 pyh1a96a4e_0 conda-forge/noarch 100 KB + google-auth-httplib2 0.1.0 pyhd8ed1ab_1 conda-forge/noarch 13 KB + google-cloud-core 2.3.1 pyhd8ed1ab_0 conda-forge/noarch 27 KB + google-cloud-storage 2.10.0 pyh1a96a4e_0 conda-forge/noarch 81 KB + google-crc32c 1.1.2 py36h25ea633_0 conda-forge/osx-64 Cached + google-resumable-media 2.3.3 pyhd8ed1ab_0 conda-forge/noarch 42 KB + googleapis-common-protos 1.53.0 py36h79c6626_0 conda-forge/osx-64 Cached + graphite2 1.3.13 h2e338ed_1001 conda-forge/osx-64 Cached + graphviz 2.42.3 h98dfb87_0 conda-forge/osx-64 Cached + grpcio 1.38.1 py36h8d587b5_0 conda-forge/osx-64 Cached + gsl 2.2.1 blas_openblash47a8a8e_5 conda-forge/osx-64 Cached + harfbuzz 2.4.0 h92b87b8_1 conda-forge/osx-64 1 MB + hmmer 3.3.2 h7133b54_4 bioconda/osx-64 15 MB + htslib 1.10.2 h862b14c_0 bioconda/osx-64 1 MB + httplib2 0.22.0 pyhd8ed1ab_0 conda-forge/noarch 93 KB + icu 58.2 h0a44026_1000 conda-forge/osx-64 Cached + idba 1.1.3 1 bioconda/osx-64 Cached + idna 3.4 pyhd8ed1ab_0 conda-forge/noarch 55 KB + idna_ssl 1.1.0 pyhd8ed1ab_1002 conda-forge/noarch Cached + imagemagick 7.0.8_54 pl526h65d2115_0 conda-forge/osx-64 2 MB + imagesize 1.4.1 pyhd8ed1ab_0 conda-forge/noarch 10 KB + importlib-metadata 4.8.1 py36h79c6626_0 conda-forge/osx-64 Cached + ipython_genutils 0.2.0 py_1 conda-forge/noarch Cached + isa-l 2.30.0 h0d85af4_4 conda-forge/osx-64 174 KB + jbig 2.1 h0d85af4_2003 conda-forge/osx-64 Cached + jinja2 3.0.3 pyhd8ed1ab_0 conda-forge/noarch Cached + jmespath 0.10.0 pyh9f0ad1d_0 conda-forge/noarch Cached + joblib 1.3.0 pyhd8ed1ab_0 conda-forge/noarch 216 KB + jpeg 9e hb7f2c08_3 conda-forge/osx-64 226 KB + jsonschema 4.1.2 pyhd8ed1ab_0 conda-forge/noarch Cached + jupyter_core 4.8.1 py36h79c6626_0 conda-forge/osx-64 Cached + kiwisolver 1.3.1 py36hc61eee1_1 conda-forge/osx-64 Cached + krb5 1.16.4 h1752a42_0 conda-forge/osx-64 Cached + lcms2 2.11 h11f7e16_1 conda-forge/osx-64 Cached + ld64_osx-64 609 hfd63004_13 conda-forge/osx-64 1 MB + libblas 3.9.0 15_osx64_openblas conda-forge/osx-64 12 KB + libcblas 3.9.0 15_osx64_openblas conda-forge/osx-64 12 KB + libclang-cpp14 14.0.6 default_hdb78580_1 conda-forge/osx-64 11 MB + libcrc32c 1.1.2 he49afe7_0 conda-forge/osx-64 Cached + libcroco 0.6.13 hc484408_0 conda-forge/osx-64 115 KB + libcurl 7.68.0 h709d2b2_0 conda-forge/osx-64 Cached + libcxx 16.0.6 hd57cbcb_0 conda-forge/osx-64 1 MB + libdeflate 1.18 hac1461d_0 conda-forge/osx-64 65 KB + libedit 3.1.20191231 h0678c8f_2 conda-forge/osx-64 103 KB + libffi 3.2.1 hb1e8313_1007 conda-forge/osx-64 Cached + libgcc 4.8.5 hdbeacc1_10 conda-forge/osx-64 Cached + libgfortran 3.0.1 0 conda-forge/osx-64 Cached + libglib 2.66.3 h2575888_0 conda-forge/osx-64 3 MB + libiconv 1.17 hac89ed1_0 conda-forge/osx-64 1 MB + libidn2 2.3.4 hb7f2c08_0 conda-forge/osx-64 170 KB + liblapack 3.9.0 15_osx64_openblas conda-forge/osx-64 12 KB + libllvm14 14.0.6 hc8e404f_3 conda-forge/osx-64 21 MB + libopenblas 0.3.20 h9a5756b_0 pkgs/main/osx-64 5 MB + libpng 1.6.39 ha978bb4_0 conda-forge/osx-64 265 KB + libprotobuf 3.18.0 hcf210ce_1 conda-forge/osx-64 Cached + librsvg 2.44.14 h423af4f_0 conda-forge/osx-64 2 MB + libsodium 1.0.18 hbcb3906_1 conda-forge/osx-64 Cached + libssh2 1.10.0 h7535e13_3 conda-forge/osx-64 222 KB + libtiff 4.1.0 h2ef1027_2 pkgs/main/osx-64 425 KB + libunistring 0.9.10 h0d85af4_0 conda-forge/osx-64 1 MB + libwebp 1.0.2 h20df551_3 conda-forge/osx-64 Cached + libxcb 1.15 hb7f2c08_0 conda-forge/osx-64 306 KB + libxml2 2.9.9 hd80cff7_2 conda-forge/osx-64 Cached + libzlib 1.2.13 h8a1eda9_5 conda-forge/osx-64 58 KB + llvm-openmp 16.0.6 hff08bdf_0 conda-forge/osx-64 289 KB + llvm-tools 14.0.6 hc8e404f_3 conda-forge/osx-64 11 MB + make 4.3 h22f3db7_1 conda-forge/osx-64 Cached + markupsafe 2.0.1 py36hfa26744_0 conda-forge/osx-64 Cached + matplotlib-base 3.3.4 py36h4ea959b_0 conda-forge/osx-64 Cached + maxbin2 2.2.7 h589c0e0_3 bioconda/osx-64 Cached + megahit 1.2.9 h2ed8fcc_1 bioconda/osx-64 2 MB + metabat2 2.15 h72337ff_1 bioconda/osx-64 1 MB + mpi 1.0 mpich conda-forge/osx-64 4 KB + mpich 3.2.1 ha90c164_1014 conda-forge/osx-64 4 MB + multidict 5.2.0 py36hfa26744_0 conda-forge/osx-64 Cached + nbformat 5.1.3 pyhd8ed1ab_0 conda-forge/noarch Cached + ncbi-vdb 2.11.0 h589c0e0_1 bioconda/osx-64 8 MB + ncurses 6.2 h2e338ed_4 conda-forge/osx-64 881 KB + networkx 2.7 pyhd8ed1ab_0 conda-forge/noarch 2 MB + nose 1.3.7 py_1006 conda-forge/noarch Cached + numpy 1.19.5 py36h08b5fde_2 conda-forge/osx-64 Cached + oauth2client 4.1.3 py_0 conda-forge/noarch Cached + olefile 0.46 pyh9f0ad1d_1 conda-forge/noarch Cached + openblas 0.2.20 8 conda-forge/osx-64 Cached + openjpeg 2.3.1 h6cbf5cd_3 conda-forge/osx-64 Cached + openssl 1.1.1u h8a1eda9_0 conda-forge/osx-64 2 MB + packaging 21.3 pyhd8ed1ab_0 conda-forge/noarch Cached + pandas 1.1.5 py36h2be6da3_0 conda-forge/osx-64 Cached + pandoc 3.1.3 h9d075a6_0 conda-forge/osx-64 15 MB + pango 1.40.14 h0da9b22_1005 conda-forge/osx-64 518 KB + paramiko 2.12.0 pyhd8ed1ab_0 conda-forge/noarch 141 KB + pcre 8.45 he49afe7_0 conda-forge/osx-64 Cached + perl 5.26.2 hbcb3906_1008 conda-forge/osx-64 Cached + perl-archive-tar 2.32 pl526_0 bioconda/osx-64 31 KB + perl-base 2.23 pl526_1 bioconda/osx-64 Cached + perl-business-isbn 3.004 pl526_0 bioconda/osx-64 Cached + perl-business-isbn-data 20140910.003 pl526_0 bioconda/osx-64 Cached + perl-carp 1.38 pl526_3 bioconda/osx-64 Cached + perl-common-sense 3.74 pl526_2 bioconda/osx-64 15 KB + perl-compress-raw-bzip2 2.087 pl526h6de7cb9_0 bioconda/osx-64 47 KB + perl-compress-raw-zlib 2.087 pl526h770b8ee_0 bioconda/osx-64 Cached + perl-constant 1.33 pl526_1 bioconda/osx-64 Cached + perl-data-dumper 2.173 pl526_0 bioconda/osx-64 Cached + perl-digest-hmac 1.03 pl526_3 bioconda/osx-64 Cached + perl-digest-md5 2.55 pl526_0 bioconda/osx-64 Cached + perl-encode 2.88 pl526_1 bioconda/osx-64 Cached + perl-encode-locale 1.05 pl526_6 bioconda/osx-64 Cached + perl-exporter 5.72 pl526_1 bioconda/osx-64 Cached + perl-exporter-tiny 1.002001 pl526_0 bioconda/osx-64 23 KB + perl-extutils-makemaker 7.36 pl526_1 bioconda/osx-64 Cached + perl-file-listing 6.04 pl526_1 bioconda/osx-64 Cached + perl-html-parser 3.72 pl526h04f5b5a_5 bioconda/osx-64 Cached + perl-html-tagset 3.20 pl526_3 bioconda/osx-64 Cached + perl-http-cookies 6.04 pl526_0 bioconda/osx-64 Cached + perl-http-daemon 6.01 pl526_1 bioconda/osx-64 Cached + perl-http-date 6.02 pl526_3 bioconda/osx-64 Cached + perl-http-message 6.18 pl526_0 bioconda/osx-64 Cached + perl-http-negotiate 6.01 pl526_3 bioconda/osx-64 Cached + perl-io-compress 2.087 pl526h6de7cb9_0 bioconda/osx-64 81 KB + perl-io-html 1.001 pl526_2 bioconda/osx-64 Cached + perl-io-socket-ssl 2.066 pl526_0 bioconda/osx-64 Cached + perl-io-zlib 1.10 pl526_2 bioconda/osx-64 9 KB + perl-json 4.02 pl526_0 bioconda/osx-64 52 KB + perl-json-xs 2.34 pl526h04f5b5a_3 bioconda/osx-64 61 KB + perl-libwww-perl 6.39 pl526_0 bioconda/noarch Cached + perl-list-moreutils 0.428 pl526_1 bioconda/osx-64 28 KB + perl-list-moreutils-xs 0.428 pl526_0 bioconda/osx-64 40 KB + perl-lwp-mediatypes 6.04 pl526_0 bioconda/osx-64 Cached + perl-lwp-simple 6.15 pl526h470a237_4 bioconda/osx-64 Cached + perl-mime-base64 3.15 pl526_1 bioconda/osx-64 Cached + perl-net-http 6.19 pl526_0 bioconda/noarch Cached + perl-net-ssleay 1.88 pl526hb1dc21d_0 bioconda/osx-64 Cached + perl-ntlm 1.09 pl526_4 bioconda/osx-64 Cached + perl-parent 0.236 pl526_1 bioconda/osx-64 Cached + perl-pathtools 3.75 pl526h1de35cc_1 bioconda/osx-64 39 KB + perl-scalar-list-utils 1.52 pl526h01d97ff_0 bioconda/osx-64 35 KB + perl-storable 3.15 pl526h1de35cc_0 bioconda/osx-64 Cached + perl-time-local 1.28 pl526_1 bioconda/osx-64 Cached + perl-try-tiny 0.30 pl526_1 bioconda/osx-64 Cached + perl-types-serialiser 1.0 pl526_2 bioconda/osx-64 10 KB + perl-uri 1.76 pl526_0 bioconda/osx-64 Cached + perl-www-robotrules 6.02 pl526_3 bioconda/osx-64 Cached + perl-xsloader 0.24 pl526_0 bioconda/osx-64 Cached + pillow 8.1.0 py36hc04f27d_1 conda-forge/osx-64 Cached + pip 21.3.1 pyhd8ed1ab_0 conda-forge/noarch Cached + pixman 0.38.0 h01d97ff_1003 conda-forge/osx-64 611 KB + pkg-config 0.29.2 ha3d46e9_1008 conda-forge/osx-64 263 KB + ply 3.11 py_1 conda-forge/noarch Cached + prettytable 2.5.0 pyhd8ed1ab_0 conda-forge/noarch 25 KB + protobuf 3.18.0 py36hefe7e0e_0 conda-forge/osx-64 Cached + psutil 5.8.0 py36hfa26744_1 conda-forge/osx-64 Cached + pthread-stubs 0.4 hc929b4f_1001 conda-forge/osx-64 Cached + pulp 2.5.1 py36h79c6626_0 conda-forge/osx-64 Cached + pyasn1 0.4.8 py_0 conda-forge/noarch Cached + pyasn1-modules 0.2.7 py_0 conda-forge/noarch Cached + pycparser 2.21 pyhd8ed1ab_0 conda-forge/noarch Cached + pygments 2.14.0 pyhd8ed1ab_0 conda-forge/noarch 805 KB + pygraphviz 1.6 py36h55e09c2_1 conda-forge/osx-64 Cached + pynacl 1.4.0 py36hfa26744_2 conda-forge/osx-64 Cached + pyopenssl 22.0.0 pyhd8ed1ab_1 conda-forge/noarch 120 KB + pyparsing 3.1.0 pyhd8ed1ab_0 conda-forge/noarch 87 KB + pyrsistent 0.17.3 py36hfa26744_2 conda-forge/osx-64 Cached + pysftp 0.2.9 py_1 conda-forge/noarch Cached + pysocks 1.7.1 py36h79c6626_3 conda-forge/osx-64 Cached + python 3.6.7 h8dc6b48_1004 conda-forge/osx-64 Cached + python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge/noarch Cached + python-irodsclient 1.1.8 pyhd8ed1ab_0 conda-forge/noarch 152 KB + python_abi 3.6 2_cp36m conda-forge/osx-64 Cached + pytz 2023.3 pyhd8ed1ab_0 conda-forge/noarch 182 KB + pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge/noarch Cached + pyyaml 5.4.1 py36hfa26744_1 conda-forge/osx-64 Cached + r-askpass 1.1 r35h17f1fa6_1 conda-forge/osx-64 Cached + r-assertthat 0.2.1 r35h6115d3f_1 conda-forge/noarch Cached + r-backports 1.1.6 r35h17f1fa6_1 conda-forge/osx-64 Cached + r-base 3.5.1 he1ce5cd_1005 conda-forge/osx-64 Cached + r-base64enc 0.1_3 r35h17f1fa6_1003 conda-forge/osx-64 Cached + r-bitops 1.0_6 r35h17f1fa6_1003 conda-forge/osx-64 Cached + r-broom 0.5.6 r35h6115d3f_0 conda-forge/noarch Cached + r-callr 3.4.3 r35h6115d3f_0 conda-forge/noarch Cached + r-catools 1.17.1.4 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-cellranger 1.1.0 r35h6115d3f_1002 conda-forge/noarch Cached + r-cli 2.0.2 r35h6115d3f_0 conda-forge/noarch Cached + r-clipr 0.7.0 r35h6115d3f_0 conda-forge/noarch Cached + r-colorspace 1.4_1 r35h17f1fa6_1 conda-forge/osx-64 Cached + r-crayon 1.3.4 r35h6115d3f_1002 conda-forge/noarch Cached + r-curl 4.3 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-dbi 1.1.0 r35h6115d3f_0 conda-forge/noarch Cached + r-dbplyr 1.4.3 r35h6115d3f_0 conda-forge/noarch Cached + r-desc 1.2.0 r35h6115d3f_1002 conda-forge/noarch Cached + r-digest 0.6.25 r35hc5da6b9_1 conda-forge/osx-64 Cached + r-dplyr 0.8.5 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-ellipsis 0.3.0 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-evaluate 0.14 r35h6115d3f_1 conda-forge/noarch Cached + r-fansi 0.4.1 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-farver 2.0.3 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-forcats 0.5.0 r35h6115d3f_0 conda-forge/noarch Cached + r-fs 1.4.1 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-gdata 2.18.0 r35h6115d3f_1002 conda-forge/noarch Cached + r-generics 0.0.2 r35h6115d3f_1002 conda-forge/noarch Cached + r-ggplot2 3.3.0 r35h6115d3f_0 conda-forge/noarch Cached + r-gh 1.1.0 r35h6115d3f_0 conda-forge/noarch Cached + r-git2r 0.26.1 r35h8d49edc_1 conda-forge/osx-64 Cached + r-glue 1.4.0 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-gplots 3.0.3 r35h6115d3f_0 conda-forge/noarch Cached + r-gridextra 2.3 r35h6115d3f_1002 conda-forge/noarch Cached + r-gtable 0.3.0 r35h6115d3f_2 conda-forge/noarch Cached + r-gtools 3.8.2 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-haven 2.2.0 r35hee97c7f_0 conda-forge/osx-64 Cached + r-highr 0.8 r35h6115d3f_1 conda-forge/noarch Cached + r-hms 0.5.3 r35h6115d3f_0 conda-forge/noarch Cached + r-htmltools 0.4.0 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-httr 1.4.1 r35h6115d3f_1 conda-forge/noarch Cached + r-hunspell 3.0 r35hf99fc2c_1001 conda-forge/osx-64 Cached + r-ini 0.3.1 r35h6115d3f_1002 conda-forge/noarch Cached + r-isoband 0.2.1 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-isocodes 2020.03.16 r35h6115d3f_0 conda-forge/noarch Cached + r-janeaustenr 0.1.5 r35h6115d3f_1002 conda-forge/noarch Cached + r-jsonlite 1.6.1 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-kernsmooth 2.23_15 r35haf69682_1004 conda-forge/osx-64 Cached + r-knitr 1.28 r35h6115d3f_0 conda-forge/noarch Cached + r-labeling 0.3 r35h6115d3f_1002 conda-forge/noarch Cached + r-lattice 0.20_41 r35h17f1fa6_1 conda-forge/osx-64 Cached + r-lifecycle 0.2.0 r35h6115d3f_0 conda-forge/noarch Cached + r-lubridate 1.7.8 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-magrittr 1.5 r35h6115d3f_1002 conda-forge/noarch Cached + r-markdown 1.1 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-mass 7.3_51.6 r35h17f1fa6_1 conda-forge/osx-64 Cached + r-matrix 1.2_18 r35h26f5615_2 conda-forge/osx-64 Cached + r-mgcv 1.8_31 r35h26f5615_0 conda-forge/osx-64 Cached + r-mime 0.9 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-modelr 0.1.7 r35h6115d3f_0 conda-forge/noarch Cached + r-munsell 0.5.0 r35h6115d3f_1002 conda-forge/noarch Cached + r-nlme 3.1_141 r35haf69682_1 conda-forge/osx-64 Cached + r-openssl 1.4.1 r35h9d0ceee_0 conda-forge/osx-64 Cached + r-pillar 1.4.3 r35h6115d3f_0 conda-forge/noarch Cached + r-pkgbuild 1.0.7 r35h6115d3f_0 conda-forge/noarch Cached + r-pkgconfig 2.0.3 r35h6115d3f_0 conda-forge/noarch Cached + r-pkgload 1.0.2 r35hc5da6b9_1001 conda-forge/osx-64 Cached + r-plogr 0.2.0 r35h6115d3f_1002 conda-forge/noarch Cached + r-plyr 1.8.6 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-praise 1.0.0 r35h6115d3f_1003 conda-forge/noarch Cached + r-prettyunits 1.1.1 r35h6115d3f_0 conda-forge/noarch Cached + r-processx 3.4.2 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-progress 1.2.2 r35h6115d3f_1 conda-forge/noarch Cached + r-ps 1.3.2 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-purrr 0.3.4 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-r6 2.4.1 r35h6115d3f_0 conda-forge/noarch Cached + r-rcolorbrewer 1.1_2 r35h6115d3f_1002 conda-forge/noarch Cached + r-rcpp 1.0.4.6 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-readr 1.3.1 r35hf99fc2c_1002 conda-forge/osx-64 Cached + r-readxl 1.3.1 r35hee97c7f_3 conda-forge/osx-64 Cached + r-rematch 1.0.1 r35h6115d3f_1002 conda-forge/noarch Cached + r-rematch2 2.1.2 r35h6115d3f_0 conda-forge/noarch Cached + r-reprex 0.3.0 r35h6115d3f_1 conda-forge/noarch Cached + r-reshape2 1.4.4 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-rlang 0.4.5 r35h17f1fa6_2 conda-forge/osx-64 Cached + r-rmarkdown 1.10 r351hf348343_0 pkgs/r/osx-64 2 MB + r-rprojroot 1.3_2 r35h6115d3f_1002 conda-forge/noarch Cached + r-rstudioapi 0.11 r35h6115d3f_0 conda-forge/noarch Cached + r-rvest 0.3.5 r35h6115d3f_0 conda-forge/noarch Cached + r-scales 1.1.0 r35h6115d3f_0 conda-forge/noarch Cached + r-selectr 0.4_2 r35h6115d3f_0 conda-forge/noarch Cached + r-snowballc 0.7.0 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-stopwords 2.0 r35h6115d3f_0 conda-forge/noarch Cached + r-stringi 1.4.3 r35hf99fc2c_2 conda-forge/osx-64 Cached + r-stringr 1.4.0 r35h6115d3f_1 conda-forge/noarch Cached + r-sys 3.3 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-testthat 2.3.2 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-tibble 3.0.1 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-tidyr 1.0.2 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-tidyselect 1.0.0 r35h6115d3f_0 conda-forge/osx-64 Cached + r-tidytext 0.2.4 r35h6115d3f_0 conda-forge/noarch Cached + r-tidyverse 1.3.0 r35h6115d3f_1 conda-forge/noarch Cached + r-tinytex 0.22 r35h6115d3f_0 conda-forge/noarch Cached + r-tokenizers 0.2.1 r35hf99fc2c_1001 conda-forge/osx-64 Cached + r-usethis 1.6.1 r35h6115d3f_0 conda-forge/noarch Cached + r-utf8 1.1.4 r35h17f1fa6_1002 conda-forge/osx-64 Cached + r-vctrs 0.2.4 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-viridislite 0.3.0 r35h6115d3f_1002 conda-forge/noarch Cached + r-whisker 0.4 r35h6115d3f_0 conda-forge/noarch Cached + r-withr 2.2.0 r35h6115d3f_0 conda-forge/noarch Cached + r-xfun 0.13 r35h6115d3f_0 conda-forge/noarch Cached + r-xml2 1.3.2 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-yaml 2.2.1 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-zeallot 0.1.0 r35h6115d3f_1001 conda-forge/noarch Cached + ratelimiter 1.2.0 pyhd8ed1ab_1003 conda-forge/noarch 13 KB + readline 7.0 hcfe32e1_1001 conda-forge/osx-64 Cached + requests 2.28.1 pyhd8ed1ab_0 conda-forge/noarch 53 KB + rsa 4.9 pyhd8ed1ab_0 conda-forge/noarch 29 KB + s3transfer 0.5.2 pyhd8ed1ab_0 conda-forge/noarch 55 KB + samtools 1.10 hf7e01e7_3 bioconda/osx-64 341 KB + scikit-learn 0.24.2 py36h979b75d_1 conda-forge/osx-64 Cached + scipy 1.5.2 py36hadf427e_0 pkgs/main/osx-64 Cached + setuptools 58.0.4 py36h79c6626_2 conda-forge/osx-64 Cached + sigtool 0.1.3 h57ddcff_0 conda-forge/osx-64 209 KB + six 1.16.0 pyh6c4a22f_0 conda-forge/noarch Cached + slacker 0.14.0 py_0 conda-forge/noarch Cached + smmap 3.0.5 pyh44b312d_0 conda-forge/noarch Cached + snakemake 5.31.0 0 bioconda/noarch 7 KB + snakemake-minimal 5.31.0 py_0 bioconda/noarch 188 KB + snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge/noarch Cached + sphinx 5.1.1 pyh6c4a22f_0 conda-forge/noarch 2 MB + sphinx_rtd_theme 1.2.2 pyha770c72_0 conda-forge/noarch 2 MB + sphinxcontrib-applehelp 1.0.4 pyhd8ed1ab_0 conda-forge/noarch 29 KB + sphinxcontrib-devhelp 1.0.2 py_0 conda-forge/noarch Cached + sphinxcontrib-htmlhelp 2.0.1 pyhd8ed1ab_0 conda-forge/noarch 32 KB + sphinxcontrib-jquery 4.1 pyhd8ed1ab_0 conda-forge/noarch 110 KB + sphinxcontrib-jsmath 1.0.1 py_0 conda-forge/noarch Cached + sphinxcontrib-qthelp 1.0.3 py_0 conda-forge/noarch Cached + sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge/noarch 27 KB + sqlite 3.28.0 h9721f7c_0 conda-forge/osx-64 Cached + stone 3.3.1 pyhd8ed1ab_0 conda-forge/noarch 146 KB + tapi 1100.0.11 h9ce4665_0 conda-forge/osx-64 Cached + tar 1.34 hcb2f6ea_1 conda-forge/osx-64 434 KB + tbb 2021.9.0 hb8565cd_0 conda-forge/osx-64 155 KB + threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge/noarch 18 KB + tk 8.6.12 h5dbffcc_0 conda-forge/osx-64 3 MB + tktable 2.10 h49f0cf7_3 conda-forge/osx-64 Cached + toposort 1.7 pyhd8ed1ab_0 conda-forge/noarch Cached + tornado 6.1 py36hfa26744_1 conda-forge/osx-64 Cached + traitlets 4.3.3 pyhd8ed1ab_2 conda-forge/noarch Cached + typing-extensions 4.1.1 hd8ed1ab_0 conda-forge/noarch 8 KB + typing_extensions 4.1.1 pyha770c72_0 conda-forge/noarch 29 KB + uritemplate 4.1.1 pyhd8ed1ab_0 conda-forge/noarch Cached + urllib3 1.26.15 pyhd8ed1ab_0 conda-forge/noarch 110 KB + wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge/noarch 28 KB + wget 1.20.3 h52ee1ee_1 conda-forge/osx-64 828 KB + wheel 0.37.1 pyhd8ed1ab_0 conda-forge/noarch 31 KB + wrapt 1.13.1 py36hfa26744_0 conda-forge/osx-64 Cached + xorg-kbproto 1.0.7 h35c211d_1002 conda-forge/osx-64 Cached + xorg-libice 1.0.10 h0d85af4_0 conda-forge/osx-64 Cached + xorg-libsm 1.2.3 h0d85af4_1000 conda-forge/osx-64 Cached + xorg-libx11 1.8.6 hbd0b022_0 conda-forge/osx-64 762 KB + xorg-libxau 1.0.11 h0dc2134_0 conda-forge/osx-64 13 KB + xorg-libxdmcp 1.1.3 h35c211d_0 conda-forge/osx-64 Cached + xorg-libxext 1.3.4 hb7f2c08_2 conda-forge/osx-64 42 KB + xorg-libxrender 0.9.11 h0dc2134_0 conda-forge/osx-64 28 KB + xorg-libxt 1.3.0 h0dc2134_0 conda-forge/osx-64 194 KB + xorg-renderproto 0.11.1 h0d85af4_1002 conda-forge/osx-64 Cached + xorg-xextproto 7.3.0 hb7f2c08_1003 conda-forge/osx-64 30 KB + xorg-xproto 7.0.31 h35c211d_1007 conda-forge/osx-64 Cached + xz 5.2.6 h775f41a_0 conda-forge/osx-64 233 KB + yaml 0.2.5 h0d85af4_2 conda-forge/osx-64 82 KB + yarl 1.6.3 py36hfa26744_2 conda-forge/osx-64 Cached + zipp 3.6.0 pyhd8ed1ab_0 conda-forge/noarch Cached + zlib 1.2.13 h8a1eda9_5 conda-forge/osx-64 89 KB + zstd 1.5.2 h829000d_7 conda-forge/osx-64 396 KB Summary: Install: 419 packages Total download: 484 MB ────────────────────────────────────────────────────────────────────────────────────────────────────────── Transaction Prefix: /Users/fzorrilla/Documents/metagem/envs/metagem Updating specs: - bedtools[version='>=2.29.2'] - bwa[version='>=0.7.17'] - concoct - diamond[version='>=2.0.6'] - fastp[version='>=0.20.1'] - maxbin2[version='>=2.2.7'] - megahit[version='>=1.2.9'] - metabat2[version='>=2.15'] - r-base[version='>=3.5.1'] - r-gridextra[version='>=2.2.1'] - r-tidyverse - r-tidytext - samtools[version='>=1.9'] - snakemake[version='>=5.10.0,<5.31.1'] Package Version Build Channel Size ────────────────────────────────────────────────────────────────────────────────────────────────────────── Install: ────────────────────────────────────────────────────────────────────────────────────────────────────────── + _r-mutex 1.0.1 anacondar_1 conda-forge/noarch Cached + aioeasywebdav 2.4.0 py36h79c6626_1001 conda-forge/osx-64 Cached + aiohttp 3.7.4.post0 py36hfa26744_0 conda-forge/osx-64 Cached + alabaster 0.7.13 pyhd8ed1ab_0 conda-forge/noarch 18 KB + amply 0.1.6 pyhd8ed1ab_0 conda-forge/noarch 21 KB + appdirs 1.4.4 pyh9f0ad1d_0 conda-forge/noarch Cached + async-timeout 3.0.1 py_1000 conda-forge/noarch Cached + attrs 22.2.0 pyh71513ae_0 conda-forge/noarch 53 KB + babel 2.11.0 pyhd8ed1ab_0 conda-forge/noarch 7 MB + backports 1.0 pyhd8ed1ab_3 conda-forge/noarch 6 KB + backports.functools_lru_cache 1.6.5 pyhd8ed1ab_0 conda-forge/noarch 11 KB + bcrypt 3.2.0 py36hfa26744_1 conda-forge/osx-64 Cached + bedtools 2.31.0 h6372da2_2 bioconda/osx-64 768 KB + biopython 1.79 py36hfa26744_0 conda-forge/osx-64 Cached + blas 1.1 openblas conda-forge/osx-64 Cached + blast 2.14.0 pl5321h91c44f7_2 bioconda/osx-64 232 MB + boto3 1.21.32 pyhd8ed1ab_0 conda-forge/noarch 71 KB + botocore 1.24.32 pyhd3eb1b0_0 pkgs/main/noarch 4 MB + bowtie2 2.5.1 py36hde6f128_1 bioconda/osx-64 1 MB + brotlipy 0.7.0 py36hfa26744_1001 conda-forge/osx-64 Cached + bwa 0.7.17 h45fc8d7_11 bioconda/osx-64 222 KB + bwidget 1.9.14 h694c41f_1 conda-forge/osx-64 Cached + bzip2 1.0.8 h0d85af4_4 conda-forge/osx-64 Cached + c-ares 1.19.1 h0dc2134_0 conda-forge/osx-64 101 KB + ca-certificates 2023.5.7 h8857fd0_0 conda-forge/osx-64 145 KB + cachetools 5.0.0 pyhd8ed1ab_0 conda-forge/noarch 12 KB + cairo 1.16.0 h0ab9d94_1001 conda-forge/osx-64 1 MB + cctools_osx-64 973.0.1 hcc6d90d_13 conda-forge/osx-64 1 MB + certifi 2021.5.30 py36h79c6626_0 conda-forge/osx-64 Cached + cffi 1.14.4 py36h1b827b8_0 conda-forge/osx-64 Cached + chardet 4.0.0 py36h79c6626_1 conda-forge/osx-64 Cached + charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge/noarch 36 KB + clang 14.0.6 h694c41f_1 conda-forge/osx-64 130 KB + clang-14 14.0.6 default_hdb78580_1 conda-forge/osx-64 1005 KB + clang_osx-64 14.0.6 h3113cd8_6 conda-forge/osx-64 20 KB + clangxx 14.0.6 default_hdb78580_1 conda-forge/osx-64 130 KB + clangxx_osx-64 14.0.6 h6f97653_6 conda-forge/osx-64 19 KB + coincbc 2.10.3 h7a5a08d_3 conda-forge/osx-64 Cached + colorama 0.4.5 pyhd8ed1ab_0 conda-forge/noarch 18 KB + compiler-rt 14.0.6 h613da45_0 conda-forge/osx-64 83 KB + compiler-rt_osx-64 14.0.6 hab78ec2_0 conda-forge/noarch 15 MB + concoct 0.4.1 py36hd1ccf6d_0 bioconda/osx-64 Cached + configargparse 1.5.5 pyhd8ed1ab_0 conda-forge/noarch 40 KB + cryptography 35.0.0 py36ha6a00b0_0 conda-forge/osx-64 Cached + curl 7.68.0 h8754def_0 conda-forge/osx-64 Cached + cycler 0.11.0 pyhd8ed1ab_0 conda-forge/noarch Cached + cython 0.29.24 py36hefe7e0e_0 conda-forge/osx-64 Cached + datrie 0.8.2 py36hfa26744_2 conda-forge/osx-64 Cached + decorator 5.1.1 pyhd8ed1ab_0 conda-forge/noarch 12 KB + defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge/noarch 23 KB + diamond 2.1.8 h94ec1f5_0 bioconda/osx-64 3 MB + docutils 0.17.1 py36h79c6626_0 conda-forge/osx-64 Cached + dropbox 11.36.2 pyhd8ed1ab_0 conda-forge/noarch 956 KB + entrez-direct 16.2 h193322a_1 bioconda/osx-64 7 MB + fastp 0.23.4 h5712c04_2 bioconda/osx-64 237 KB + fftw 3.3.8 mpi_mpich_h6e18f22_1009 conda-forge/osx-64 5 MB + filechunkio 1.8 py_2 conda-forge/noarch Cached + fontconfig 2.13.1 h1027ab8_1000 conda-forge/osx-64 Cached + fraggenescan 1.31 h2413b67_6 bioconda/osx-64 1 MB + freetype 2.12.1 h3f81eb7_1 conda-forge/osx-64 586 KB + ftputil 5.0.4 pyhd8ed1ab_0 conda-forge/noarch 42 KB + gdk-pixbuf 2.36.12 h306395f_1005 conda-forge/osx-64 565 KB + gettext 0.21.1 h8a4c099_0 conda-forge/osx-64 4 MB + gfortran_osx-64 4.8.5 h22b1bf0_8 conda-forge/osx-64 Cached + ghostscript 9.54.0 h96cf925_2 conda-forge/osx-64 56 MB + giflib 5.1.7 h01d97ff_1 conda-forge/osx-64 Cached + gitdb 4.0.10 pyhd8ed1ab_0 conda-forge/noarch 50 KB + gitpython 3.1.18 pyhd8ed1ab_0 conda-forge/noarch Cached + glib 2.66.3 h519c658_0 conda-forge/osx-64 491 KB + gobject-introspection 1.66.1 py36h251bb5a_3 conda-forge/osx-64 1 MB + google-api-core 2.8.0 pyhd8ed1ab_1 conda-forge/noarch 70 KB + google-api-python-client 2.52.0 pyhd8ed1ab_0 conda-forge/noarch 5 MB + google-auth 2.22.0 pyh1a96a4e_0 conda-forge/noarch 100 KB + google-auth-httplib2 0.1.0 pyhd8ed1ab_1 conda-forge/noarch 13 KB + google-cloud-core 2.3.1 pyhd8ed1ab_0 conda-forge/noarch 27 KB + google-cloud-storage 2.10.0 pyh1a96a4e_0 conda-forge/noarch 81 KB + google-crc32c 1.1.2 py36h25ea633_0 conda-forge/osx-64 Cached + google-resumable-media 2.3.3 pyhd8ed1ab_0 conda-forge/noarch 42 KB + googleapis-common-protos 1.53.0 py36h79c6626_0 conda-forge/osx-64 Cached + graphite2 1.3.13 h2e338ed_1001 conda-forge/osx-64 Cached + graphviz 2.42.3 h98dfb87_0 conda-forge/osx-64 Cached + grpcio 1.38.1 py36h8d587b5_0 conda-forge/osx-64 Cached + gsl 2.2.1 blas_openblash47a8a8e_5 conda-forge/osx-64 Cached + harfbuzz 2.4.0 h92b87b8_1 conda-forge/osx-64 1 MB + hmmer 3.3.2 h7133b54_4 bioconda/osx-64 15 MB + htslib 1.10.2 h862b14c_0 bioconda/osx-64 1 MB + httplib2 0.22.0 pyhd8ed1ab_0 conda-forge/noarch 93 KB + icu 58.2 h0a44026_1000 conda-forge/osx-64 Cached + idba 1.1.3 1 bioconda/osx-64 Cached + idna 3.4 pyhd8ed1ab_0 conda-forge/noarch 55 KB + idna_ssl 1.1.0 pyhd8ed1ab_1002 conda-forge/noarch Cached + imagemagick 7.0.8_54 pl526h65d2115_0 conda-forge/osx-64 2 MB + imagesize 1.4.1 pyhd8ed1ab_0 conda-forge/noarch 10 KB + importlib-metadata 4.8.1 py36h79c6626_0 conda-forge/osx-64 Cached + ipython_genutils 0.2.0 py_1 conda-forge/noarch Cached + isa-l 2.30.0 h0d85af4_4 conda-forge/osx-64 174 KB + jbig 2.1 h0d85af4_2003 conda-forge/osx-64 Cached + jinja2 3.0.3 pyhd8ed1ab_0 conda-forge/noarch Cached + jmespath 0.10.0 pyh9f0ad1d_0 conda-forge/noarch Cached + joblib 1.3.0 pyhd8ed1ab_0 conda-forge/noarch 216 KB + jpeg 9e hb7f2c08_3 conda-forge/osx-64 226 KB + jsonschema 4.1.2 pyhd8ed1ab_0 conda-forge/noarch Cached + jupyter_core 4.8.1 py36h79c6626_0 conda-forge/osx-64 Cached + kiwisolver 1.3.1 py36hc61eee1_1 conda-forge/osx-64 Cached + krb5 1.16.4 h1752a42_0 conda-forge/osx-64 Cached + lcms2 2.11 h11f7e16_1 conda-forge/osx-64 Cached + ld64_osx-64 609 hfd63004_13 conda-forge/osx-64 1 MB + libblas 3.9.0 15_osx64_openblas conda-forge/osx-64 12 KB + libcblas 3.9.0 15_osx64_openblas conda-forge/osx-64 12 KB + libclang-cpp14 14.0.6 default_hdb78580_1 conda-forge/osx-64 11 MB + libcrc32c 1.1.2 he49afe7_0 conda-forge/osx-64 Cached + libcroco 0.6.13 hc484408_0 conda-forge/osx-64 115 KB + libcurl 7.68.0 h709d2b2_0 conda-forge/osx-64 Cached + libcxx 16.0.6 hd57cbcb_0 conda-forge/osx-64 1 MB + libdeflate 1.18 hac1461d_0 conda-forge/osx-64 65 KB + libedit 3.1.20191231 h0678c8f_2 conda-forge/osx-64 103 KB + libffi 3.2.1 hb1e8313_1007 conda-forge/osx-64 Cached + libgcc 4.8.5 hdbeacc1_10 conda-forge/osx-64 Cached + libgfortran 3.0.1 0 conda-forge/osx-64 Cached + libglib 2.66.3 h2575888_0 conda-forge/osx-64 3 MB + libiconv 1.17 hac89ed1_0 conda-forge/osx-64 1 MB + libidn2 2.3.4 hb7f2c08_0 conda-forge/osx-64 170 KB + liblapack 3.9.0 15_osx64_openblas conda-forge/osx-64 12 KB + libllvm14 14.0.6 hc8e404f_3 conda-forge/osx-64 21 MB + libopenblas 0.3.20 h9a5756b_0 pkgs/main/osx-64 5 MB + libpng 1.6.39 ha978bb4_0 conda-forge/osx-64 265 KB + libprotobuf 3.18.0 hcf210ce_1 conda-forge/osx-64 Cached + librsvg 2.44.14 h423af4f_0 conda-forge/osx-64 2 MB + libsodium 1.0.18 hbcb3906_1 conda-forge/osx-64 Cached + libssh2 1.10.0 h7535e13_3 conda-forge/osx-64 222 KB + libtiff 4.1.0 h2ef1027_2 pkgs/main/osx-64 425 KB + libunistring 0.9.10 h0d85af4_0 conda-forge/osx-64 1 MB + libwebp 1.0.2 h20df551_3 conda-forge/osx-64 Cached + libxcb 1.15 hb7f2c08_0 conda-forge/osx-64 306 KB + libxml2 2.9.9 hd80cff7_2 conda-forge/osx-64 Cached + libzlib 1.2.13 h8a1eda9_5 conda-forge/osx-64 58 KB + llvm-openmp 16.0.6 hff08bdf_0 conda-forge/osx-64 289 KB + llvm-tools 14.0.6 hc8e404f_3 conda-forge/osx-64 11 MB + make 4.3 h22f3db7_1 conda-forge/osx-64 Cached + markupsafe 2.0.1 py36hfa26744_0 conda-forge/osx-64 Cached + matplotlib-base 3.3.4 py36h4ea959b_0 conda-forge/osx-64 Cached + maxbin2 2.2.7 h589c0e0_3 bioconda/osx-64 Cached + megahit 1.2.9 h2ed8fcc_1 bioconda/osx-64 2 MB + metabat2 2.15 h72337ff_1 bioconda/osx-64 1 MB + mpi 1.0 mpich conda-forge/osx-64 4 KB + mpich 3.2.1 ha90c164_1014 conda-forge/osx-64 4 MB + multidict 5.2.0 py36hfa26744_0 conda-forge/osx-64 Cached + nbformat 5.1.3 pyhd8ed1ab_0 conda-forge/noarch Cached + ncbi-vdb 2.11.0 h589c0e0_1 bioconda/osx-64 8 MB + ncurses 6.2 h2e338ed_4 conda-forge/osx-64 881 KB + networkx 2.7 pyhd8ed1ab_0 conda-forge/noarch 2 MB + nose 1.3.7 py_1006 conda-forge/noarch Cached + numpy 1.19.5 py36h08b5fde_2 conda-forge/osx-64 Cached + oauth2client 4.1.3 py_0 conda-forge/noarch Cached + olefile 0.46 pyh9f0ad1d_1 conda-forge/noarch Cached + openblas 0.2.20 8 conda-forge/osx-64 Cached + openjpeg 2.3.1 h6cbf5cd_3 conda-forge/osx-64 Cached + openssl 1.1.1u h8a1eda9_0 conda-forge/osx-64 2 MB + packaging 21.3 pyhd8ed1ab_0 conda-forge/noarch Cached + pandas 1.1.5 py36h2be6da3_0 conda-forge/osx-64 Cached + pandoc 3.1.3 h9d075a6_0 conda-forge/osx-64 15 MB + pango 1.40.14 h0da9b22_1005 conda-forge/osx-64 518 KB + paramiko 2.12.0 pyhd8ed1ab_0 conda-forge/noarch 141 KB + pcre 8.45 he49afe7_0 conda-forge/osx-64 Cached + perl 5.26.2 hbcb3906_1008 conda-forge/osx-64 Cached + perl-archive-tar 2.32 pl526_0 bioconda/osx-64 31 KB + perl-base 2.23 pl526_1 bioconda/osx-64 Cached + perl-business-isbn 3.004 pl526_0 bioconda/osx-64 Cached + perl-business-isbn-data 20140910.003 pl526_0 bioconda/osx-64 Cached + perl-carp 1.38 pl526_3 bioconda/osx-64 Cached + perl-common-sense 3.74 pl526_2 bioconda/osx-64 15 KB + perl-compress-raw-bzip2 2.087 pl526h6de7cb9_0 bioconda/osx-64 47 KB + perl-compress-raw-zlib 2.087 pl526h770b8ee_0 bioconda/osx-64 Cached + perl-constant 1.33 pl526_1 bioconda/osx-64 Cached + perl-data-dumper 2.173 pl526_0 bioconda/osx-64 Cached + perl-digest-hmac 1.03 pl526_3 bioconda/osx-64 Cached + perl-digest-md5 2.55 pl526_0 bioconda/osx-64 Cached + perl-encode 2.88 pl526_1 bioconda/osx-64 Cached + perl-encode-locale 1.05 pl526_6 bioconda/osx-64 Cached + perl-exporter 5.72 pl526_1 bioconda/osx-64 Cached + perl-exporter-tiny 1.002001 pl526_0 bioconda/osx-64 23 KB + perl-extutils-makemaker 7.36 pl526_1 bioconda/osx-64 Cached + perl-file-listing 6.04 pl526_1 bioconda/osx-64 Cached + perl-html-parser 3.72 pl526h04f5b5a_5 bioconda/osx-64 Cached + perl-html-tagset 3.20 pl526_3 bioconda/osx-64 Cached + perl-http-cookies 6.04 pl526_0 bioconda/osx-64 Cached + perl-http-daemon 6.01 pl526_1 bioconda/osx-64 Cached + perl-http-date 6.02 pl526_3 bioconda/osx-64 Cached + perl-http-message 6.18 pl526_0 bioconda/osx-64 Cached + perl-http-negotiate 6.01 pl526_3 bioconda/osx-64 Cached + perl-io-compress 2.087 pl526h6de7cb9_0 bioconda/osx-64 81 KB + perl-io-html 1.001 pl526_2 bioconda/osx-64 Cached + perl-io-socket-ssl 2.066 pl526_0 bioconda/osx-64 Cached + perl-io-zlib 1.10 pl526_2 bioconda/osx-64 9 KB + perl-json 4.02 pl526_0 bioconda/osx-64 52 KB + perl-json-xs 2.34 pl526h04f5b5a_3 bioconda/osx-64 61 KB + perl-libwww-perl 6.39 pl526_0 bioconda/noarch Cached + perl-list-moreutils 0.428 pl526_1 bioconda/osx-64 28 KB + perl-list-moreutils-xs 0.428 pl526_0 bioconda/osx-64 40 KB + perl-lwp-mediatypes 6.04 pl526_0 bioconda/osx-64 Cached + perl-lwp-simple 6.15 pl526h470a237_4 bioconda/osx-64 Cached + perl-mime-base64 3.15 pl526_1 bioconda/osx-64 Cached + perl-net-http 6.19 pl526_0 bioconda/noarch Cached + perl-net-ssleay 1.88 pl526hb1dc21d_0 bioconda/osx-64 Cached + perl-ntlm 1.09 pl526_4 bioconda/osx-64 Cached + perl-parent 0.236 pl526_1 bioconda/osx-64 Cached + perl-pathtools 3.75 pl526h1de35cc_1 bioconda/osx-64 39 KB + perl-scalar-list-utils 1.52 pl526h01d97ff_0 bioconda/osx-64 35 KB + perl-storable 3.15 pl526h1de35cc_0 bioconda/osx-64 Cached + perl-time-local 1.28 pl526_1 bioconda/osx-64 Cached + perl-try-tiny 0.30 pl526_1 bioconda/osx-64 Cached + perl-types-serialiser 1.0 pl526_2 bioconda/osx-64 10 KB + perl-uri 1.76 pl526_0 bioconda/osx-64 Cached + perl-www-robotrules 6.02 pl526_3 bioconda/osx-64 Cached + perl-xsloader 0.24 pl526_0 bioconda/osx-64 Cached + pillow 8.1.0 py36hc04f27d_1 conda-forge/osx-64 Cached + pip 21.3.1 pyhd8ed1ab_0 conda-forge/noarch Cached + pixman 0.38.0 h01d97ff_1003 conda-forge/osx-64 611 KB + pkg-config 0.29.2 ha3d46e9_1008 conda-forge/osx-64 263 KB + ply 3.11 py_1 conda-forge/noarch Cached + prettytable 2.5.0 pyhd8ed1ab_0 conda-forge/noarch 25 KB + protobuf 3.18.0 py36hefe7e0e_0 conda-forge/osx-64 Cached + psutil 5.8.0 py36hfa26744_1 conda-forge/osx-64 Cached + pthread-stubs 0.4 hc929b4f_1001 conda-forge/osx-64 Cached + pulp 2.5.1 py36h79c6626_0 conda-forge/osx-64 Cached + pyasn1 0.4.8 py_0 conda-forge/noarch Cached + pyasn1-modules 0.2.7 py_0 conda-forge/noarch Cached + pycparser 2.21 pyhd8ed1ab_0 conda-forge/noarch Cached + pygments 2.14.0 pyhd8ed1ab_0 conda-forge/noarch 805 KB + pygraphviz 1.6 py36h55e09c2_1 conda-forge/osx-64 Cached + pynacl 1.4.0 py36hfa26744_2 conda-forge/osx-64 Cached + pyopenssl 22.0.0 pyhd8ed1ab_1 conda-forge/noarch 120 KB + pyparsing 3.1.0 pyhd8ed1ab_0 conda-forge/noarch 87 KB + pyrsistent 0.17.3 py36hfa26744_2 conda-forge/osx-64 Cached + pysftp 0.2.9 py_1 conda-forge/noarch Cached + pysocks 1.7.1 py36h79c6626_3 conda-forge/osx-64 Cached + python 3.6.7 h8dc6b48_1004 conda-forge/osx-64 Cached + python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge/noarch Cached + python-irodsclient 1.1.8 pyhd8ed1ab_0 conda-forge/noarch 152 KB + python_abi 3.6 2_cp36m conda-forge/osx-64 Cached + pytz 2023.3 pyhd8ed1ab_0 conda-forge/noarch 182 KB + pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge/noarch Cached + pyyaml 5.4.1 py36hfa26744_1 conda-forge/osx-64 Cached + r-askpass 1.1 r35h17f1fa6_1 conda-forge/osx-64 Cached + r-assertthat 0.2.1 r35h6115d3f_1 conda-forge/noarch Cached + r-backports 1.1.6 r35h17f1fa6_1 conda-forge/osx-64 Cached + r-base 3.5.1 he1ce5cd_1005 conda-forge/osx-64 Cached + r-base64enc 0.1_3 r35h17f1fa6_1003 conda-forge/osx-64 Cached + r-bitops 1.0_6 r35h17f1fa6_1003 conda-forge/osx-64 Cached + r-broom 0.5.6 r35h6115d3f_0 conda-forge/noarch Cached + r-callr 3.4.3 r35h6115d3f_0 conda-forge/noarch Cached + r-catools 1.17.1.4 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-cellranger 1.1.0 r35h6115d3f_1002 conda-forge/noarch Cached + r-cli 2.0.2 r35h6115d3f_0 conda-forge/noarch Cached + r-clipr 0.7.0 r35h6115d3f_0 conda-forge/noarch Cached + r-colorspace 1.4_1 r35h17f1fa6_1 conda-forge/osx-64 Cached + r-crayon 1.3.4 r35h6115d3f_1002 conda-forge/noarch Cached + r-curl 4.3 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-dbi 1.1.0 r35h6115d3f_0 conda-forge/noarch Cached + r-dbplyr 1.4.3 r35h6115d3f_0 conda-forge/noarch Cached + r-desc 1.2.0 r35h6115d3f_1002 conda-forge/noarch Cached + r-digest 0.6.25 r35hc5da6b9_1 conda-forge/osx-64 Cached + r-dplyr 0.8.5 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-ellipsis 0.3.0 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-evaluate 0.14 r35h6115d3f_1 conda-forge/noarch Cached + r-fansi 0.4.1 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-farver 2.0.3 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-forcats 0.5.0 r35h6115d3f_0 conda-forge/noarch Cached + r-fs 1.4.1 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-gdata 2.18.0 r35h6115d3f_1002 conda-forge/noarch Cached + r-generics 0.0.2 r35h6115d3f_1002 conda-forge/noarch Cached + r-ggplot2 3.3.0 r35h6115d3f_0 conda-forge/noarch Cached + r-gh 1.1.0 r35h6115d3f_0 conda-forge/noarch Cached + r-git2r 0.26.1 r35h8d49edc_1 conda-forge/osx-64 Cached + r-glue 1.4.0 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-gplots 3.0.3 r35h6115d3f_0 conda-forge/noarch Cached + r-gridextra 2.3 r35h6115d3f_1002 conda-forge/noarch Cached + r-gtable 0.3.0 r35h6115d3f_2 conda-forge/noarch Cached + r-gtools 3.8.2 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-haven 2.2.0 r35hee97c7f_0 conda-forge/osx-64 Cached + r-highr 0.8 r35h6115d3f_1 conda-forge/noarch Cached + r-hms 0.5.3 r35h6115d3f_0 conda-forge/noarch Cached + r-htmltools 0.4.0 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-httr 1.4.1 r35h6115d3f_1 conda-forge/noarch Cached + r-hunspell 3.0 r35hf99fc2c_1001 conda-forge/osx-64 Cached + r-ini 0.3.1 r35h6115d3f_1002 conda-forge/noarch Cached + r-isoband 0.2.1 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-isocodes 2020.03.16 r35h6115d3f_0 conda-forge/noarch Cached + r-janeaustenr 0.1.5 r35h6115d3f_1002 conda-forge/noarch Cached + r-jsonlite 1.6.1 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-kernsmooth 2.23_15 r35haf69682_1004 conda-forge/osx-64 Cached + r-knitr 1.28 r35h6115d3f_0 conda-forge/noarch Cached + r-labeling 0.3 r35h6115d3f_1002 conda-forge/noarch Cached + r-lattice 0.20_41 r35h17f1fa6_1 conda-forge/osx-64 Cached + r-lifecycle 0.2.0 r35h6115d3f_0 conda-forge/noarch Cached + r-lubridate 1.7.8 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-magrittr 1.5 r35h6115d3f_1002 conda-forge/noarch Cached + r-markdown 1.1 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-mass 7.3_51.6 r35h17f1fa6_1 conda-forge/osx-64 Cached + r-matrix 1.2_18 r35h26f5615_2 conda-forge/osx-64 Cached + r-mgcv 1.8_31 r35h26f5615_0 conda-forge/osx-64 Cached + r-mime 0.9 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-modelr 0.1.7 r35h6115d3f_0 conda-forge/noarch Cached + r-munsell 0.5.0 r35h6115d3f_1002 conda-forge/noarch Cached + r-nlme 3.1_141 r35haf69682_1 conda-forge/osx-64 Cached + r-openssl 1.4.1 r35h9d0ceee_0 conda-forge/osx-64 Cached + r-pillar 1.4.3 r35h6115d3f_0 conda-forge/noarch Cached + r-pkgbuild 1.0.7 r35h6115d3f_0 conda-forge/noarch Cached + r-pkgconfig 2.0.3 r35h6115d3f_0 conda-forge/noarch Cached + r-pkgload 1.0.2 r35hc5da6b9_1001 conda-forge/osx-64 Cached + r-plogr 0.2.0 r35h6115d3f_1002 conda-forge/noarch Cached + r-plyr 1.8.6 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-praise 1.0.0 r35h6115d3f_1003 conda-forge/noarch Cached + r-prettyunits 1.1.1 r35h6115d3f_0 conda-forge/noarch Cached + r-processx 3.4.2 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-progress 1.2.2 r35h6115d3f_1 conda-forge/noarch Cached + r-ps 1.3.2 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-purrr 0.3.4 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-r6 2.4.1 r35h6115d3f_0 conda-forge/noarch Cached + r-rcolorbrewer 1.1_2 r35h6115d3f_1002 conda-forge/noarch Cached + r-rcpp 1.0.4.6 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-readr 1.3.1 r35hf99fc2c_1002 conda-forge/osx-64 Cached + r-readxl 1.3.1 r35hee97c7f_3 conda-forge/osx-64 Cached + r-rematch 1.0.1 r35h6115d3f_1002 conda-forge/noarch Cached + r-rematch2 2.1.2 r35h6115d3f_0 conda-forge/noarch Cached + r-reprex 0.3.0 r35h6115d3f_1 conda-forge/noarch Cached + r-reshape2 1.4.4 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-rlang 0.4.5 r35h17f1fa6_2 conda-forge/osx-64 Cached + r-rmarkdown 1.10 r351hf348343_0 pkgs/r/osx-64 2 MB + r-rprojroot 1.3_2 r35h6115d3f_1002 conda-forge/noarch Cached + r-rstudioapi 0.11 r35h6115d3f_0 conda-forge/noarch Cached + r-rvest 0.3.5 r35h6115d3f_0 conda-forge/noarch Cached + r-scales 1.1.0 r35h6115d3f_0 conda-forge/noarch Cached + r-selectr 0.4_2 r35h6115d3f_0 conda-forge/noarch Cached + r-snowballc 0.7.0 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-stopwords 2.0 r35h6115d3f_0 conda-forge/noarch Cached + r-stringi 1.4.3 r35hf99fc2c_2 conda-forge/osx-64 Cached + r-stringr 1.4.0 r35h6115d3f_1 conda-forge/noarch Cached + r-sys 3.3 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-testthat 2.3.2 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-tibble 3.0.1 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-tidyr 1.0.2 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-tidyselect 1.0.0 r35h6115d3f_0 conda-forge/osx-64 Cached + r-tidytext 0.2.4 r35h6115d3f_0 conda-forge/noarch Cached + r-tidyverse 1.3.0 r35h6115d3f_1 conda-forge/noarch Cached + r-tinytex 0.22 r35h6115d3f_0 conda-forge/noarch Cached + r-tokenizers 0.2.1 r35hf99fc2c_1001 conda-forge/osx-64 Cached + r-usethis 1.6.1 r35h6115d3f_0 conda-forge/noarch Cached + r-utf8 1.1.4 r35h17f1fa6_1002 conda-forge/osx-64 Cached + r-vctrs 0.2.4 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-viridislite 0.3.0 r35h6115d3f_1002 conda-forge/noarch Cached + r-whisker 0.4 r35h6115d3f_0 conda-forge/noarch Cached + r-withr 2.2.0 r35h6115d3f_0 conda-forge/noarch Cached + r-xfun 0.13 r35h6115d3f_0 conda-forge/noarch Cached + r-xml2 1.3.2 r35hc5da6b9_0 conda-forge/osx-64 Cached + r-yaml 2.2.1 r35h17f1fa6_0 conda-forge/osx-64 Cached + r-zeallot 0.1.0 r35h6115d3f_1001 conda-forge/noarch Cached + ratelimiter 1.2.0 pyhd8ed1ab_1003 conda-forge/noarch 13 KB + readline 7.0 hcfe32e1_1001 conda-forge/osx-64 Cached + requests 2.28.1 pyhd8ed1ab_0 conda-forge/noarch 53 KB + rsa 4.9 pyhd8ed1ab_0 conda-forge/noarch 29 KB + s3transfer 0.5.2 pyhd8ed1ab_0 conda-forge/noarch 55 KB + samtools 1.10 hf7e01e7_3 bioconda/osx-64 341 KB + scikit-learn 0.24.2 py36h979b75d_1 conda-forge/osx-64 Cached + scipy 1.5.2 py36hadf427e_0 pkgs/main/osx-64 Cached + setuptools 58.0.4 py36h79c6626_2 conda-forge/osx-64 Cached + sigtool 0.1.3 h57ddcff_0 conda-forge/osx-64 209 KB + six 1.16.0 pyh6c4a22f_0 conda-forge/noarch Cached + slacker 0.14.0 py_0 conda-forge/noarch Cached + smmap 3.0.5 pyh44b312d_0 conda-forge/noarch Cached + snakemake 5.31.0 0 bioconda/noarch 7 KB + snakemake-minimal 5.31.0 py_0 bioconda/noarch 188 KB + snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge/noarch Cached + sphinx 5.1.1 pyh6c4a22f_0 conda-forge/noarch 2 MB + sphinx_rtd_theme 1.2.2 pyha770c72_0 conda-forge/noarch 2 MB + sphinxcontrib-applehelp 1.0.4 pyhd8ed1ab_0 conda-forge/noarch 29 KB + sphinxcontrib-devhelp 1.0.2 py_0 conda-forge/noarch Cached + sphinxcontrib-htmlhelp 2.0.1 pyhd8ed1ab_0 conda-forge/noarch 32 KB + sphinxcontrib-jquery 4.1 pyhd8ed1ab_0 conda-forge/noarch 110 KB + sphinxcontrib-jsmath 1.0.1 py_0 conda-forge/noarch Cached + sphinxcontrib-qthelp 1.0.3 py_0 conda-forge/noarch Cached + sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge/noarch 27 KB + sqlite 3.28.0 h9721f7c_0 conda-forge/osx-64 Cached + stone 3.3.1 pyhd8ed1ab_0 conda-forge/noarch 146 KB + tapi 1100.0.11 h9ce4665_0 conda-forge/osx-64 Cached + tar 1.34 hcb2f6ea_1 conda-forge/osx-64 434 KB + tbb 2021.9.0 hb8565cd_0 conda-forge/osx-64 155 KB + threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge/noarch 18 KB + tk 8.6.12 h5dbffcc_0 conda-forge/osx-64 3 MB + tktable 2.10 h49f0cf7_3 conda-forge/osx-64 Cached + toposort 1.7 pyhd8ed1ab_0 conda-forge/noarch Cached + tornado 6.1 py36hfa26744_1 conda-forge/osx-64 Cached + traitlets 4.3.3 pyhd8ed1ab_2 conda-forge/noarch Cached + typing-extensions 4.1.1 hd8ed1ab_0 conda-forge/noarch 8 KB + typing_extensions 4.1.1 pyha770c72_0 conda-forge/noarch 29 KB + uritemplate 4.1.1 pyhd8ed1ab_0 conda-forge/noarch Cached + urllib3 1.26.15 pyhd8ed1ab_0 conda-forge/noarch 110 KB + wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge/noarch 28 KB + wget 1.20.3 h52ee1ee_1 conda-forge/osx-64 828 KB + wheel 0.37.1 pyhd8ed1ab_0 conda-forge/noarch 31 KB + wrapt 1.13.1 py36hfa26744_0 conda-forge/osx-64 Cached + xorg-kbproto 1.0.7 h35c211d_1002 conda-forge/osx-64 Cached + xorg-libice 1.0.10 h0d85af4_0 conda-forge/osx-64 Cached + xorg-libsm 1.2.3 h0d85af4_1000 conda-forge/osx-64 Cached + xorg-libx11 1.8.6 hbd0b022_0 conda-forge/osx-64 762 KB + xorg-libxau 1.0.11 h0dc2134_0 conda-forge/osx-64 13 KB + xorg-libxdmcp 1.1.3 h35c211d_0 conda-forge/osx-64 Cached + xorg-libxext 1.3.4 hb7f2c08_2 conda-forge/osx-64 42 KB + xorg-libxrender 0.9.11 h0dc2134_0 conda-forge/osx-64 28 KB + xorg-libxt 1.3.0 h0dc2134_0 conda-forge/osx-64 194 KB + xorg-renderproto 0.11.1 h0d85af4_1002 conda-forge/osx-64 Cached + xorg-xextproto 7.3.0 hb7f2c08_1003 conda-forge/osx-64 30 KB + xorg-xproto 7.0.31 h35c211d_1007 conda-forge/osx-64 Cached + xz 5.2.6 h775f41a_0 conda-forge/osx-64 233 KB + yaml 0.2.5 h0d85af4_2 conda-forge/osx-64 82 KB + yarl 1.6.3 py36hfa26744_2 conda-forge/osx-64 Cached + zipp 3.6.0 pyhd8ed1ab_0 conda-forge/noarch Cached + zlib 1.2.13 h8a1eda9_5 conda-forge/osx-64 89 KB + zstd 1.5.2 h829000d_7 conda-forge/osx-64 396 KB Summary: Install: 419 packages Total download: 484 MB ────────────────────────────────────────────────────────────────────────────────────────────────────────── Finished xorg-libxau (00m:00s) 13 KB 110 KB/s Finished libzlib (00m:00s) 58 KB 331 KB/s Finished xz (00m:00s) 233 KB 1 MB/s Finished jpeg (00m:00s) 226 KB 1 MB/s Finished libdeflate (00m:00s) 65 KB 233 KB/s Finished pixman (00m:00s) 611 KB 2 MB/s Finished libedit (00m:00s) 103 KB 280 KB/s Finished ncurses (00m:00s) 881 KB 2 MB/s Finished tbb (00m:00s) 155 KB 379 KB/s Finished libunistring (00m:00s) 1 MB 3 MB/s Finished libxcb (00m:00s) 306 KB 612 KB/s Finished tar (00m:00s) 434 KB 709 KB/s Finished sigtool (00m:00s) 209 KB 324 KB/s Finished xorg-libxext (00m:00s) 42 KB 52 KB/s Finished ld64_osx-64 (00m:00s) 1 MB 989 KB/s Finished clangxx (00m:00s) 130 KB 120 KB/s Finished backports (00m:00s) 6 KB 5 KB/s Finished attrs (00m:00s) 53 KB 43 KB/s Finished xorg-libx11 (00m:00s) 762 KB 602 KB/s Finished sphinxcontrib-serializinghtml (00m:00s) 27 KB 21 KB/s Finished imagesize (00m:00s) 10 KB 7 KB/s Finished threadpoolctl (00m:00s) 18 KB 13 KB/s Finished configargparse (00m:00s) 40 KB 28 KB/s Finished cachetools (00m:00s) 12 KB 8 KB/s Finished rsa (00m:00s) 29 KB 19 KB/s Finished pygments (00m:00s) 805 KB 490 KB/s Finished perl-scalar-list-utils (00m:00s) 35 KB 21 KB/s Finished perl-io-zlib (00m:00s) 9 KB 5 KB/s Finished pandoc (00m:01s) 15 MB 8 MB/s Finished libclang-cpp14 (00m:01s) 11 MB 5 MB/s Finished perl-types-serialiser (00m:00s) 10 KB 5 KB/s Finished bedtools (00m:00s) 768 KB 326 KB/s Finished htslib (00m:00s) 1 MB 618 KB/s Finished perl-list-moreutils (00m:00s) 28 KB 11 KB/s Finished perl-archive-tar (00m:00s) 31 KB 12 KB/s Finished glib (00m:00s) 491 KB 180 KB/s Finished samtools (00m:00s) 341 KB 122 KB/s Finished babel (00m:01s) 7 MB 2 MB/s Finished ncbi-vdb (00m:00s) 8 MB 3 MB/s Finished clangxx_osx-64 (00m:00s) 19 KB 6 KB/s Finished google-resumable-media (00m:00s) 42 KB 13 KB/s Finished pango (00m:00s) 518 KB 161 KB/s Finished gdk-pixbuf (00m:00s) 565 KB 176 KB/s Finished libopenblas (00m:00s) 5 MB 2 MB/s Finished google-auth-httplib2 (00m:00s) 13 KB 4 KB/s Finished cairo (00m:00s) 1 MB 416 KB/s Finished python-irodsclient (00m:00s) 152 KB 45 KB/s Finished google-cloud-storage (00m:00s) 81 KB 24 KB/s Finished google-auth (00m:00s) 100 KB 29 KB/s Finished google-cloud-core (00m:00s) 27 KB 8 KB/s Finished c-ares (00m:00s) 101 KB 29 KB/s Finished libiconv (00m:00s) 1 MB 383 KB/s Finished libpng (00m:00s) 265 KB 73 KB/s Finished freetype (00m:00s) 586 KB 156 KB/s Finished libglib (00m:00s) 3 MB 639 KB/s Finished botocore (00m:01s) 4 MB 946 KB/s Finished gettext (00m:00s) 4 MB 875 KB/s Finished wheel (00m:00s) 31 KB 7 KB/s Finished r-rmarkdown (00m:01s) 2 MB 457 KB/s Finished pyparsing (00m:00s) 87 KB 18 KB/s Finished clang-14 (00m:00s) 1005 KB 208 KB/s Finished idna (00m:00s) 55 KB 11 KB/s Finished decorator (00m:00s) 12 KB 2 KB/s Finished colorama (00m:00s) 18 KB 4 KB/s Finished gitdb (00m:00s) 50 KB 10 KB/s Finished xorg-libxrender (00m:00s) 28 KB 6 KB/s Finished perl-exporter-tiny (00m:00s) 23 KB 4 KB/s Finished stone (00m:00s) 146 KB 28 KB/s Finished perl-list-moreutils-xs (00m:00s) 40 KB 8 KB/s Finished perl-json-xs (00m:00s) 61 KB 11 KB/s Finished compiler-rt (00m:00s) 83 KB 15 KB/s Finished libcroco (00m:00s) 115 KB 20 KB/s Finished libllvm14 (00m:02s) 21 MB 4 MB/s Finished gobject-introspection (00m:00s) 1 MB 231 KB/s Finished imagemagick (00m:00s) 2 MB 332 KB/s Finished paramiko (00m:00s) 141 KB 21 KB/s Finished requests (00m:00s) 53 KB 8 KB/s Finished google-api-core (00m:00s) 70 KB 10 KB/s Finished entrez-direct (00m:01s) 7 MB 1 MB/s Finished boto3 (00m:00s) 71 KB 10 KB/s Finished sphinx_rtd_theme (00m:00s) 2 MB 359 KB/s Finished xorg-xextproto (00m:00s) 30 KB 4 KB/s Finished libcxx (00m:00s) 1 MB 155 KB/s Finished zlib (00m:00s) 89 KB 12 KB/s Finished mpi (00m:00s) 4 KB 604 B/s Finished libidn2 (00m:00s) 170 KB 23 KB/s Finished wget (00m:00s) 828 KB 108 KB/s Finished openssl (00m:00s) 2 MB 222 KB/s Finished sphinxcontrib-htmlhelp (00m:00s) 32 KB 4 KB/s Finished pytz (00m:00s) 182 KB 24 KB/s Finished defusedxml (00m:00s) 23 KB 3 KB/s Finished backports.functools_lru_cache (00m:00s) 11 KB 1 KB/s Finished wcwidth (00m:00s) 28 KB 4 KB/s Finished hmmer (00m:02s) 15 MB 2 MB/s Finished perl-compress-raw-bzip2 (00m:00s) 47 KB 6 KB/s Finished cctools_osx-64 (00m:00s) 1 MB 137 KB/s Finished clang_osx-64 (00m:00s) 20 KB 2 KB/s Finished metabat2 (00m:00s) 1 MB 145 KB/s Finished prettytable (00m:00s) 25 KB 3 KB/s Finished bowtie2 (00m:00s) 1 MB 165 KB/s Finished diamond (00m:00s) 3 MB 358 KB/s Finished harfbuzz (00m:00s) 1 MB 148 KB/s Finished snakemake-minimal (00m:00s) 188 KB 22 KB/s Finished isa-l (00m:00s) 174 KB 20 KB/s Finished pkg-config (00m:00s) 263 KB 30 KB/s Finished sphinx (00m:00s) 2 MB 180 KB/s Finished libssh2 (00m:00s) 222 KB 24 KB/s Finished google-api-python-client (00m:00s) 5 MB 545 KB/s Finished alabaster (00m:00s) 18 KB 2 KB/s Finished clang (00m:00s) 130 KB 14 KB/s Finished typing-extensions (00m:00s) 8 KB 858 B/s Finished typing_extensions (00m:00s) 29 KB 3 KB/s Finished perl-pathtools (00m:00s) 39 KB 4 KB/s Finished libcblas (00m:00s) 12 KB 1 KB/s Finished tk (00m:00s) 3 MB 363 KB/s Finished amply (00m:00s) 21 KB 2 KB/s Finished megahit (00m:00s) 2 MB 168 KB/s Finished s3transfer (00m:00s) 55 KB 6 KB/s Finished fraggenescan (00m:00s) 1 MB 141 KB/s Finished dropbox (00m:00s) 956 KB 98 KB/s Finished yaml (00m:00s) 82 KB 8 KB/s Finished joblib (00m:00s) 216 KB 22 KB/s Finished ftputil (00m:00s) 42 KB 4 KB/s Finished perl-common-sense (00m:00s) 15 KB 2 KB/s Finished libblas (00m:00s) 12 KB 1 KB/s Finished perl-io-compress (00m:00s) 81 KB 8 KB/s Finished pyopenssl (00m:00s) 120 KB 12 KB/s Finished ca-certificates (00m:00s) 145 KB 14 KB/s Finished networkx (00m:00s) 2 MB 148 KB/s Finished charset-normalizer (00m:00s) 36 KB 3 KB/s Finished httplib2 (00m:00s) 93 KB 9 KB/s Finished perl-json (00m:00s) 52 KB 5 KB/s Finished fftw (00m:01s) 5 MB 482 KB/s Finished snakemake (00m:00s) 7 KB 584 B/s Finished librsvg (00m:00s) 2 MB 206 KB/s Finished sphinxcontrib-applehelp (00m:00s) 29 KB 2 KB/s Finished bwa (00m:00s) 222 KB 18 KB/s Finished urllib3 (00m:00s) 110 KB 9 KB/s Finished zstd (00m:00s) 396 KB 32 KB/s Finished ratelimiter (00m:00s) 13 KB 1 KB/s Finished liblapack (00m:00s) 12 KB 982 B/s Finished mpich (00m:01s) 4 MB 320 KB/s Finished xorg-libxt (00m:00s) 194 KB 15 KB/s Finished llvm-tools (00m:02s) 11 MB 822 KB/s Finished libtiff (00m:00s) 425 KB 32 KB/s Finished fastp (00m:00s) 237 KB 17 KB/s Finished llvm-openmp (00m:00s) 289 KB 21 KB/s Finished sphinxcontrib-jquery (00m:00s) 110 KB 8 KB/s Finished compiler-rt_osx-64 (00m:03s) 15 MB 946 KB/s Finished ghostscript (00m:07s) 56 MB 3 MB/s Finished blast (00m:19s) 232 MB 10 MB/s Downloading [====================================================================================================] (00m:43s) 19.91 MB/s Extracting [====================================================================================================] (00m:43s) 151 / 151 Preparing transaction: done Verifying transaction: done Executing transaction: done # # To activate this environment, use # # $ conda activate /Users/fzorrilla/Documents/metagem/envs/metagem # # To deactivate an active environment, use # # $ conda deactivate ```

As for the metawrap env, you can refer to their own installation details , and there is also some documentation in the above-linked metaGEM manual setup wiki. This should work:

mamba create -y -n metawrap-env python=2.7
conda activate metawrap-env

conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda config --add channels ursky

mamba install biopython blas=2.5 blast=2.6.0 bmtagger bowtie2 bwa checkm-genome fastqc kraken=1.1 kraken=2.0 krona=2.7 matplotlib maxbin2 megahit metabat2 pandas prokka quast r-ggplot2 r-recommended salmon samtools=1.9 seaborn spades trim-galore

Hope this helps!

transition-bio-1 commented 1 year ago

Amazing! Will give this a shot over the weekend. Thank you so much for being so responsive.