diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml index b9a293752..43935f67b 100644 --- a/deployments/biology/image/environment.yml +++ b/deployments/biology/image/environment.yml @@ -9,6 +9,7 @@ dependencies: - nb_conda_kernels=2.3.1 # Packages from bioconda for IB134L +- biopython==1.81 - bwa=0.7.12 - samtools=1.3.1 - mafft=7.471 @@ -19,10 +20,10 @@ dependencies: - paml=4.9 #- repeatmasker=4.0.9 - trimmomatic=0.39 -- blast=2.12.0 +- blast=2.14.1 - fastqc=0.11.9 - phyml=3.3.20200621 -- sra-tools=2.11 +- sra-tools=3.0.8 - hisat2=2.2.1 - subread=2.0.1 - plink=1.90b6.21 @@ -30,7 +31,7 @@ dependencies: - syncthing==1.18.6 # Packages for IB120/201/CCB210 -- sympy=1.6.2 +- sympy=1.10.1 # Packages from bioconda for BioE-131, Fall 2020, Issue #1885 - bowtie2=2.4.2 @@ -46,8 +47,8 @@ dependencies: # pedagogy packages -- scipy=1.7.1 -- pandas=1.3.2 +- scipy=1.10.1 +- pandas=2.0.2 - seaborn=0.11.2 # compbio BioE c146, Fall 22 and into the future, issue 3785 diff --git a/deployments/biology/image/install-mambaforge.bash b/deployments/biology/image/install-mambaforge.bash index 13f431411..0344ddcfa 100644 --- a/deployments/biology/image/install-mambaforge.bash +++ b/deployments/biology/image/install-mambaforge.bash @@ -3,7 +3,7 @@ set -ex cd $(dirname $0) -MAMBAFORGE_VERSION=4.10.3-7 +MAMBAFORGE_VERSION='23.3.1-1' URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/mambaforge-installer.sh diff --git a/deployments/data8/image/install-mambaforge.bash b/deployments/data8/image/install-mambaforge.bash index 13f431411..0344ddcfa 100755 --- a/deployments/data8/image/install-mambaforge.bash +++ b/deployments/data8/image/install-mambaforge.bash @@ -3,7 +3,7 @@ set -ex cd $(dirname $0) -MAMBAFORGE_VERSION=4.10.3-7 +MAMBAFORGE_VERSION='23.3.1-1' URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/mambaforge-installer.sh diff --git a/deployments/datahub/images/default/install-mambaforge.bash b/deployments/datahub/images/default/install-mambaforge.bash index 13f431411..0344ddcfa 100755 --- a/deployments/datahub/images/default/install-mambaforge.bash +++ b/deployments/datahub/images/default/install-mambaforge.bash @@ -3,7 +3,7 @@ set -ex cd $(dirname $0) -MAMBAFORGE_VERSION=4.10.3-7 +MAMBAFORGE_VERSION='23.3.1-1' URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/mambaforge-installer.sh diff --git a/deployments/ischool/image/install-mambaforge.bash b/deployments/ischool/image/install-mambaforge.bash index 13f431411..0344ddcfa 100755 --- a/deployments/ischool/image/install-mambaforge.bash +++ b/deployments/ischool/image/install-mambaforge.bash @@ -3,7 +3,7 @@ set -ex cd $(dirname $0) -MAMBAFORGE_VERSION=4.10.3-7 +MAMBAFORGE_VERSION='23.3.1-1' URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/mambaforge-installer.sh diff --git a/deployments/shiny/image/install-mambaforge.bash b/deployments/shiny/image/install-mambaforge.bash index 13f431411..0344ddcfa 100755 --- a/deployments/shiny/image/install-mambaforge.bash +++ b/deployments/shiny/image/install-mambaforge.bash @@ -3,7 +3,7 @@ set -ex cd $(dirname $0) -MAMBAFORGE_VERSION=4.10.3-7 +MAMBAFORGE_VERSION='23.3.1-1' URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/mambaforge-installer.sh