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Update cd-hit and mmseq installation18
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breimanntools committed Jun 27, 2024
1 parent 3dbcae3 commit 2a3d405
Showing 1 changed file with 4 additions and 1 deletion.
5 changes: 4 additions & 1 deletion .github/workflows/main.yml
Original file line number Diff line number Diff line change
Expand Up @@ -63,6 +63,7 @@ jobs:
sudo apt-get install -y cd-hit mmseqs2
- name: Set up WSL and compile cd-hit
if: runner.os == 'Windows'
shell: bash
run: |
sudo apt update
Expand All @@ -74,6 +75,7 @@ jobs:
sudo cp cd-hit /usr/local/bin/
- name: Install mmseqs2 (Windows)
if: runner.os == 'Windows'
shell: pwsh
run: |
curl -L -o mmseqs2.zip https://mmseqs.com/latest/mmseqs-win64.zip
Expand All @@ -88,6 +90,7 @@ jobs:
Get-ChildItem $mmseqsBinPath
- name: Verify cd-hit installation (WSL)
if: runner.os == 'Windows'
shell: bash
run: |
if ! command -v cd-hit &> /dev/null
Expand All @@ -98,6 +101,7 @@ jobs:
cd-hit --version
- name: Verify mmseqs2 installation
if: runner.os == 'Windows'
shell: pwsh
run: |
$mmseqsBinPath = "$Env:USERPROFILE\mmseqs\mmseqs-win64"
Expand All @@ -111,7 +115,6 @@ jobs:
mmseqs --version
}
- name: Run Tests
run: pytest tests
env:
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