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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,84 +1,93 @@ | ||
| channels: | ||
| - bioconda | ||
| - conda-forge | ||
| dependencies: | ||
| - python=3.11.* | ||
| - pip=22.2.* | ||
|
|
||
| # Package to allow Jupyter Notebook or JupyterLab applications in one conda env to access other kernels (e.g. qiime2) | ||
| - nb_conda_kernels=2.3.1 | ||
| - bioconda | ||
| - conda-forge | ||
|
|
||
| # proxy web applications | ||
| - jupyter-server-proxy==4.2.0 | ||
| - jupyter-rsession-proxy==2.0.1 | ||
| dependencies: | ||
| # Items required for basic level functionality | ||
| - gh-scoped-creds==4.1 | ||
| # DH-418, bunch of stuff fails to install if git is set higher to this e.g. git==2.47.1 | ||
| - git==2.38.1 | ||
| - jupyter-archive==3.4.0 | ||
| - jupyter-resource-usage==1.1.0 | ||
| - jupyter-server-proxy==4.4.0 | ||
| - jupyter_server==2.15.0 | ||
| - jupyterhub==5.2.1 | ||
| - jupyterlab==4.3.4 | ||
| - jupyterlab-git==0.50.2 | ||
| - jupyterlab_rise==0.43.1 | ||
| - jupytext==1.16.6 | ||
| - nbgitpuller==1.2.1 | ||
| - notebook==7.3.2 | ||
| - pip==24.3.1 | ||
| - python==3.11.* | ||
|
|
||
| # Packages from bioconda for IB134L | ||
| - bwa=0.7.18 | ||
| - bcftools==1.16 | ||
| - samtools=1.3.1 | ||
| - mafft=7.471 | ||
| - emboss=6.6.0 | ||
| - augustus=3.5.0 | ||
| - raxml-ng=1.0.1 | ||
| - structure=2.3.4 | ||
| - paml=4.9 | ||
| #- repeatmasker=4.0.9 | ||
| - seqtk | ||
| - trimmomatic=0.39 | ||
| - blast=2.12.0 | ||
| - fastqc=0.11.9 | ||
| - phyml=3.3.20200621 | ||
| - sra-tools=2.11 | ||
| - hisat2=2.2.1 | ||
| - subread=2.0.6 | ||
| - plink=1.90b6.21 | ||
| # Package to allow Jupyter Notebook or JupyterLab applications in one conda env to access other kernels (e.g. qiime2) | ||
| - nb_conda_kernels==2.5.1 | ||
| - jupyter-rsession-proxy==2.3.0 | ||
|
|
||
| - syncthing==1.18.6 | ||
| # Packages from bioconda for IB134L | ||
| - augustus==3.5.0 | ||
| - bcftools==1.16 | ||
| - blast==2.12.0 | ||
| - bwa==0.7.18 | ||
| - emboss==6.6.0 | ||
| - fastqc==0.11.9 | ||
| - hisat2==2.2.1 | ||
| - mafft==7.471 | ||
| - paml==4.9 | ||
| - plink==1.90b6.21 | ||
| - phyml==3.3.20200621 | ||
| - raxml-ng==1.0.1 | ||
| - samtools==1.3.1 | ||
| - seqtk==1.4 | ||
| - sra-tools==2.11 | ||
| - structure==2.3.4 | ||
| - subread==2.0.6 | ||
| - syncthing==1.18.6 | ||
| - trimmomatic==0.39 | ||
|
|
||
| # Packages for IB120/201/CCB210 | ||
| - sympy=1.12 | ||
| # Packages for IB120/201/CCB210 | ||
| - sympy==1.12 | ||
|
|
||
| # Packages from bioconda for BioE-131, Fall 2020, Issue #1885 | ||
| - bowtie2==2.5.4 | ||
| - spades=3.14.1 | ||
| # Packages from bioconda for BioE-131, Fall 2020, Issue #1885 | ||
| - bowtie2==2.5.4 | ||
| - spades==3.14.1 | ||
|
|
||
| # Packages for MCB280A, Spring 2022 | ||
| - bedtools=2.30.0 | ||
| # Packages for MCB280A, Spring 2022 | ||
| - bedtools==2.30.0 | ||
| - datascience==0.17.6 | ||
|
|
||
| # Packages from bioconda for BIO1B | ||
| - raxml=8.2.* | ||
| - muscle=3.8.* | ||
| - dendropy=4.4.* | ||
| # Packages from bioconda for BIO1B | ||
| - dendropy==4.4.0 | ||
| - muscle==3.8.1551 | ||
| - raxml==8.2.13 | ||
|
|
||
| # pedagogy packages | ||
| - scipy=1.11. | ||
| - pandas=2.2.2 | ||
| - seaborn=0.13.2 | ||
| # pedagogy packages | ||
| - pandas==2.2.2 | ||
| - scipy==1.15.1 | ||
| - seaborn==0.13.2 | ||
|
|
||
| # compbio BioE c146, Fall 22 and into the future, issue 3785 | ||
| - scikit-learn=1.2.2 | ||
| # compbio BioE c146, Fall 22 and into the future, issue 3785 | ||
| - scikit-learn==1.2.2 | ||
|
|
||
| # bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048 | ||
| - traitlets=5.9.* | ||
| # bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048 | ||
| - traitlets==5.14.3 | ||
|
|
||
| # for MCELLBI201B (FA24) https://github.com/berkeley-dsep-infra/datahub/issues/5988 | ||
| - macs2==2.2.9.1 | ||
| # for MCELLBI201B (FA24) https://github.com/berkeley-dsep-infra/datahub/issues/5988 | ||
| - macs2==2.2.9.1 | ||
|
|
||
| # For https://github.com/berkeley-dsep-infra/datahub/issues/1846 | ||
| # Conda does not have these | ||
| - pip: | ||
| - -r infra-requirements.txt | ||
| # MCB280A, Spring 2022 | ||
| - pybedtools==0.10.0 | ||
| # removed for PR https://github.com/berkeley-dsep-infra/datahub/pull/4406 - macs2==2.2.7.1 | ||
| - geonomics==1.4.1 | ||
| - nlmpy==1.2.0 | ||
| - datascience==0.17.6 | ||
|
|
||
| # Packages for MCB-160L iss #3942 | ||
| - allensdk==2.16.2 | ||
| - otter-grader==3.1.4 | ||
| # for exporting notebooks to pdf | ||
| - nbconvert[webpdf]==7.16.4 | ||
| - nb2pdf==0.6.2 | ||
| - nbpdfexport==0.2.1 | ||
| # For https://github.com/berkeley-dsep-infra/datahub/issues/1846 | ||
| # Conda does not have these | ||
| - pip: | ||
| # MCB280A, Spring 2022 | ||
| - geonomics==1.4.1 | ||
| - nlmpy==1.2.0 | ||
| - pybedtools==0.10.0 | ||
| # Packages for MCB-160L iss #3942 | ||
| # DH-418 requires pandas 1.5.3, conflicts with otter-grader which needs 2.2.2 | ||
| # - allensdk==2.16.2 | ||
| - otter-grader==6.0.4 | ||
| # for exporting notebooks to pdf | ||
| - nbconvert[webpdf]==7.16.5 | ||
| - nb2pdf==0.6.2 | ||
| - nbpdfexport==0.2.1 |
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