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[DH-166] bumping mambaforge to something current #5175

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[DH-166] bumping mambaforge to something current #5175

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f728f82
bumping mambaforge to something current
shaneknapp Oct 30, 2023
85deaa9
bump python, begin dependency hell
shaneknapp Oct 30, 2023
cdcfaef
bump scipy
shaneknapp Oct 30, 2023
4e875f9
more dep hell as usual
shaneknapp Oct 30, 2023
fd027f0
more dep hell as usual
shaneknapp Oct 30, 2023
62a8892
le sigh le bowtie
shaneknapp Oct 30, 2023
e99a899
last try today
shaneknapp Oct 31, 2023
7e2eb5b
maybe one more
shaneknapp Oct 31, 2023
b6da08d
blast!
shaneknapp Oct 31, 2023
bed69fd
debump python
shaneknapp Oct 31, 2023
af166cb
oh my aching brain
shaneknapp Oct 31, 2023
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11 changes: 6 additions & 5 deletions deployments/biology/image/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -19,18 +20,18 @@ 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

- 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
Expand All @@ -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
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2 changes: 1 addition & 1 deletion deployments/biology/image/install-mambaforge.bash
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion deployments/data8/image/install-mambaforge.bash
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion deployments/datahub/images/default/install-mambaforge.bash
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion deployments/ischool/image/install-mambaforge.bash
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion deployments/shiny/image/install-mambaforge.bash
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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