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Merged
bbimber merged 4 commits into from
Jul 17, 2024
Merged

Backport changes in BimberLab org #300

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d28a5fc
Add --break-system-packages to pip commands
bbimber Jul 3, 2024
5902217
Merge pull request #284 from BimberLab/fb_pip
bbimber Jul 3, 2024
cc126b4
Merge pull request #287 from LabKey/develop
bbimber Jul 14, 2024
a9ea0c3
Merge develop to develop
Jul 16, 2024
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4 changes: 2 additions & 2 deletions SequenceAnalysis/pipeline_code/sequence_tools_install.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -842,9 +842,9 @@ then
install ./cutadapt-1.8.1/bin/_preamble.py ${LKTOOLS_DIR}/_preamble.py
cp -R ./cutadapt-1.8.1/cutadapt ${LKTOOLS_DIR}/cutadapt
else
$PIP_EXE install --user cutadapt==4.2
$PIP_EXE install --user --break-system-packages cutadapt==4.2
$PIP_EXE show cutadapt
$PIP_EXE install --user pyinstaller
$PIP_EXE install --user --break-system-packages pyinstaller
$PIP_EXE show pyinstaller
~/.local/bin/pyinstaller --onefile --clean ~/.local/bin/cutadapt
cp ./dist/cutadapt ${LKTOOLS_DIR}/cutadapt
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