M2 MacOS Installation Troubles about biostar-handbook HOT 8 OPEN

Thank you very much I did try with anaconda and still did not work. I have pasted the entire process below, I am sorry for the mess, please see if there is anything i did wrong. I appreciate it, thank you. Last login: Wed Jan 3 14:03:54 on ttys000 ***@***.*** ~ $ mkdir -p ~/bin ***@***.*** ~ $ curl -Ls https://micromamba.snakepit.net/api/micromamba/osx-64/latest | tar -xj bin/micromamba ***@***.*** ~ $ ***@***.*** ~ $ ./bin/micromamba shell init -s bash -p ~/micromamba -q ***@***.*** ~ $ curl -s http://data.biostarhandbook.com/install/biostar.sh > ~/.biostar.sh ***@***.*** ~ $ echo "source ~/.biostar.sh" >> ~/.bashrc ***@***.*** ~ $ echo "source ~/.bashrc" >> ~/.bash_profile ***@***.*** ~ $ conda config prepend channels conda-forge ***@***.*** ~ $ conda config append channels bioconda ***@***.*** ~ $ conda config set channel_priority strict ***@***.*** ~ $ conda create -n bioinfo -y python=3.8 conda-forge/osx-64 Using cache conda-forge/noarch Using cache bioconda/osx-64 Using cache bioconda/noarch Using cache pkgs/main/osx-64 No change pkgs/r/osx-64 No change pkgs/main/noarch No change pkgs/r/noarch No change Transaction Prefix: /Users/mesfinmeshesha/micromamba/envs/bioinfo Updating specs: - python=3.8 Package Version Build Channel Size ───────────────────────────────────────────────────────────────────────────── Install: ───────────────────────────────────────────────────────────────────────────── + xz 5.2.6 h775f41a_0 conda-forge Cached + ncurses 6.4 h93d8f39_2 conda-forge Cached + bzip2 1.0.8 h10d778d_5 conda-forge Cached + libffi 3.4.2 h0d85af4_5 conda-forge Cached + libzlib 1.2.13 h8a1eda9_5 conda-forge Cached + ca-certificates 2023.11.17 h8857fd0_0 conda-forge Cached + readline 8.2 h9e318b2_1 conda-forge Cached + tk 8.6.13 h1abcd95_1 conda-forge Cached + libsqlite 3.44.2 h92b6c6a_0 conda-forge Cached + openssl 3.2.0 hd75f5a5_1 conda-forge Cached + python 3.8.18 h5ba8234_1_cpython conda-forge Cached + wheel 0.42.0 pyhd8ed1ab_0 conda-forge Cached + setuptools 69.0.3 pyhd8ed1ab_0 conda-forge Cached + pip 23.3.2 pyhd8ed1ab_0 conda-forge Cached Summary: Install: 14 packages Total download: 0 B ───────────────────────────────────────────────────────────────────────────── Transaction starting Linking xz-5.2.6-h775f41a_0 Linking ncurses-6.4-h93d8f39_2 Linking bzip2-1.0.8-h10d778d_5 Linking libffi-3.4.2-h0d85af4_5 Linking libzlib-1.2.13-h8a1eda9_5 Linking ca-certificates-2023.11.17-h8857fd0_0 Linking readline-8.2-h9e318b2_1 Linking tk-8.6.13-h1abcd95_1 Linking libsqlite-3.44.2-h92b6c6a_0 Linking openssl-3.2.0-hd75f5a5_1 Linking python-3.8.18-h5ba8234_1_cpython Linking wheel-0.42.0-pyhd8ed1ab_0 Linking setuptools-69.0.3-pyhd8ed1ab_0 Linking pip-23.3.2-pyhd8ed1ab_0 Transaction finished To activate this environment, use: micromamba activate bioinfo Or to execute a single command in this environment, use: micromamba run -n bioinfo mycommand ***@***.*** ~ $ conda activate bioinfo (bioinfo) ***@***.*** ~ $ curl -s http://data.biostarhandbook.com/install/conda.txt | xargs conda install -q -y Retrieving notices: ...working... DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443 DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443 DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): conda.anaconda.org:443 DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): conda.anaconda.org:443 DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/notices.json HTTP/1.1" 404 None DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/notices.json HTTP/1.1" 404 None DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /conda-forge/notices.json HTTP/1.1" 404 None DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /bioconda/notices.json HTTP/1.1" 404 None done Collecting package metadata (current_repodata.json): ...working... DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): conda.anaconda.org:443 DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): conda.anaconda.org:443 DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): conda.anaconda.org:443 DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443 DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): conda.anaconda.org:443 DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443 DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443 DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443 DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/noarch/current_repodata.json HTTP/1.1" 200 None DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/osx-arm64/current_repodata.json HTTP/1.1" 304 0 DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/noarch/current_repodata.json HTTP/1.1" 200 None DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/osx-arm64/current_repodata.json HTTP/1.1" 200 None DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /bioconda/osx-arm64/current_repodata.json HTTP/1.1" 200 None DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /conda-forge/osx-arm64/current_repodata.json HTTP/1.1" 200 None DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /conda-forge/noarch/current_repodata.json HTTP/1.1" 200 None DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /bioconda/noarch/current_repodata.json HTTP/1.1" 200 None done Solving environment: ...working... unsuccessful initial attempt using frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): ...working... DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): conda.anaconda.org:443 DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): conda.anaconda.org:443 DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): conda.anaconda.org:443 DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): conda.anaconda.org:443 DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443 DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443 DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443 DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443 DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/noarch/repodata.json HTTP/1.1" 200 None DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/osx-arm64/repodata.json HTTP/1.1" 304 0 DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/osx-arm64/repodata.json HTTP/1.1" 200 None DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/noarch/repodata.json HTTP/1.1" 200 None DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /bioconda/osx-arm64/repodata.json HTTP/1.1" 200 None DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /conda-forge/noarch/repodata.json HTTP/1.1" 200 None DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /conda-forge/osx-arm64/repodata.json HTTP/1.1" 200 None DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /bioconda/noarch/repodata.json HTTP/1.1" 200 None done Solving environment: ...working... unsuccessful initial attempt using frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current channels: - blast - bcftools - bioawk - csvtk - aria2 - samtools[version='>=1.14'] - freebayes - minimap2 - bowtie2 - fastp - emboss - datamash - hisat2 - bwa - ucsc-bedgraphtobigwig - mafft - seqtk - bedtools - seqkit - subread Current channels: - https://conda.anaconda.org/conda-forge/osx-arm64 - https://conda.anaconda.org/conda-forge/noarch - https://repo.anaconda.com/pkgs/main/osx-arm64 - https://repo.anaconda.com/pkgs/main/noarch - https://repo.anaconda.com/pkgs/r/osx-arm64 - https://repo.anaconda.com/pkgs/r/noarch - https://conda.anaconda.org/bioconda/osx-arm64 - https://conda.anaconda.org/bioconda/noarch To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. (bioinfo) ***@***.*** ~ $ pip install bio --upgrade Collecting bio Using cached bio-1.6.0-py3-none-any.whl.metadata (5.1 kB) Collecting biopython>=1.80 (from bio) Downloading biopython-1.82-cp38-cp38-macosx_10_9_x86_64.whl.metadata (13 kB) Collecting requests (from bio) Using cached requests-2.31.0-py3-none-any.whl.metadata (4.6 kB) Collecting tqdm (from bio) Using cached tqdm-4.66.1-py3-none-any.whl.metadata (57 kB) Collecting mygene (from bio) Using cached mygene-3.2.2-py2.py3-none-any.whl (5.4 kB) Collecting pandas (from bio) Using cached pandas-2.0.3-cp38-cp38-macosx_10_9_x86_64.whl.metadata (18 kB) Collecting pooch (from bio) Using cached pooch-1.8.0-py3-none-any.whl.metadata (9.9 kB) Collecting gprofiler-official (from bio) Using cached gprofiler_official-1.0.0-py3-none-any.whl (9.3 kB) Collecting numpy (from biopython>=1.80->bio) Using cached numpy-1.24.4-cp38-cp38-macosx_10_9_x86_64.whl.metadata (5.6 kB) Collecting biothings-client>=0.2.6 (from mygene->bio) Using cached biothings_client-0.3.1-py2.py3-none-any.whl.metadata (9.8 kB) Collecting python-dateutil>=2.8.2 (from pandas->bio) Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) Collecting pytz>=2020.1 (from pandas->bio) Using cached pytz-2023.3.post1-py2.py3-none-any.whl.metadata (22 kB) Collecting tzdata>=2022.1 (from pandas->bio) Downloading tzdata-2023.4-py2.py3-none-any.whl.metadata (1.4 kB) Collecting platformdirs>=2.5.0 (from pooch->bio) Using cached platformdirs-4.1.0-py3-none-any.whl.metadata (11 kB) Collecting packaging>=20.0 (from pooch->bio) Using cached packaging-23.2-py3-none-any.whl.metadata (3.2 kB) Collecting charset-normalizer<4,>=2 (from requests->bio) Using cached charset_normalizer-3.3.2-cp38-cp38-macosx_10_9_x86_64.whl.metadata (33 kB) Collecting idna<4,>=2.5 (from requests->bio) Using cached idna-3.6-py3-none-any.whl.metadata (9.9 kB) Collecting urllib3<3,>=1.21.1 (from requests->bio) Using cached urllib3-2.1.0-py3-none-any.whl.metadata (6.4 kB) Collecting certifi>=2017.4.17 (from requests->bio) Using cached certifi-2023.11.17-py3-none-any.whl.metadata (2.2 kB) Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas->bio) Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) Using cached bio-1.6.0-py3-none-any.whl (279 kB) Downloading biopython-1.82-cp38-cp38-macosx_10_9_x86_64.whl (2.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.7/2.7 MB 5.9 MB/s eta 0:00:00 Using cached pandas-2.0.3-cp38-cp38-macosx_10_9_x86_64.whl (11.7 MB) Using cached pooch-1.8.0-py3-none-any.whl (62 kB) Using cached requests-2.31.0-py3-none-any.whl (62 kB) Using cached tqdm-4.66.1-py3-none-any.whl (78 kB) Using cached biothings_client-0.3.1-py2.py3-none-any.whl (29 kB) Using cached certifi-2023.11.17-py3-none-any.whl (162 kB) Using cached charset_normalizer-3.3.2-cp38-cp38-macosx_10_9_x86_64.whl (121 kB) Using cached idna-3.6-py3-none-any.whl (61 kB) Using cached numpy-1.24.4-cp38-cp38-macosx_10_9_x86_64.whl (19.8 MB) Using cached packaging-23.2-py3-none-any.whl (53 kB) Using cached platformdirs-4.1.0-py3-none-any.whl (17 kB) Using cached pytz-2023.3.post1-py2.py3-none-any.whl (502 kB) Downloading tzdata-2023.4-py2.py3-none-any.whl (346 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 346.6/346.6 kB 8.0 MB/s eta 0:00:00 Using cached urllib3-2.1.0-py3-none-any.whl (104 kB) Installing collected packages: pytz, urllib3, tzdata, tqdm, six, platformdirs, packaging, numpy, idna, charset-normalizer, certifi, requests, python-dateutil, biopython, pooch, pandas, gprofiler-official, biothings-client, mygene, bio Successfully installed bio-1.6.0 biopython-1.82 biothings-client-0.3.1 certifi-2023.11.17 charset-normalizer-3.3.2 gprofiler-official-1.0.0 idna-3.6 mygene-3.2.2 numpy-1.24.4 packaging-23.2 pandas-2.0.3 platformdirs-4.1.0 pooch-1.8.0 python-dateutil-2.8.2 pytz-2023.3.post1 requests-2.31.0 six-1.16.0 tqdm-4.66.1 tzdata-2023.4 urllib3-2.1.0 (bioinfo) ***@***.*** ~ $ yes no | sh -c "$(curl -fsSL ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)" > /dev/null (bioinfo) ***@***.*** ~ $ curl -s http://data.biostarhandbook.com/install/sratools.sh | bash (bioinfo) ***@***.*** ~ $ mkdir -p ~/bin (bioinfo) ***@***.*** ~ $ curl -s http://data.biostarhandbook.com/install/doctor.py > ~/bin/doctor.py (bioinfo) ***@***.*** ~ $ chmod +x ~/bin/doctor.py (bioinfo) ***@***.*** ~ $ ~/bin/doctor.py # Doctor! Doctor! Give me the news. # Checking symptoms ... # bwa --> ERROR # datamash --> ERROR # fastqc -h --> ERROR # hisat2 --> ERROR # seqret -h --> ERROR # featureCounts --> ERROR # efetch ... OK # esearch ... OK # samtools --> ERROR # fastq-dump --> ERROR # bowtie2 --> ERROR # bcftools --> ERROR # seqtk --> ERROR # seqkit --> ERROR # bio ... OK # fastq-dump -X 1 -Z SRR1553591 --> ERROR # # Found some problems # # Unable to run: bwa, datamash, fastqc -h, hisat2, seqret -h, featureCounts, samtools, fastq-dump, bowtie2, bcftools, seqtk, seqkit, fastq-dump -X 1 -Z SRR1553591 # # Check the Biostar Handbook for installation help. # (bioinfo) ***@***.*** ~ $

Thank you, it works now!! Mes