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Update install_software.sh
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echo "pip3 install --upgrade pip" would not upgrade pip, removing echo and quotations
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@tomas-fer
tomas-fer authored Aug 22, 2018
1 parent d1133af commit c1a1099
Showing 1 changed file with 2 additions and 2 deletions.
4 changes: 2 additions & 2 deletions install_software.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -94,7 +94,7 @@ if [[ $distribution =~ "Debian" ]]; then
echo -e "Installing 'pip2'"
$installer install -y python-pip &> pip_install.log
fi
echo "pip2 install --upgrade pip" &>> pip_install.log
pip2 install --upgrade pip &>> pip_install.log
else
if ! [ -x "$(command -v pip2.7)" ]; then
echo -e "Installing 'pip'"
Expand Down Expand Up @@ -122,7 +122,7 @@ fi
if [[ $distribution =~ "Fedora" ]]; then
python3 -m pip install --upgrade pip &>> pip3_install.log
else
echo "pip3 install --upgrade pip" &>> pip3_install.log
pip3 install --upgrade pip &>> pip3_install.log
fi

#Biopython
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3 comments on commit c1a1099

@jdhayes
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@jdhayes jdhayes commented on c1a1099 Aug 22, 2018 •
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Installs via pip seems to be failing due to the fact that the pip upgrade installs over the system /usr/bin/pip.
Something like this:
pypa/pip#5221
My install log is attached.
install.log

@tomas-fer
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Yes, this seems to be an issue only on Debian/Ubuntu. However, after a new shell is invoked (e.g., 'exec bash'), pip seems to be working...

@tomas-fer
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To prevent problems with PIP on Debian/Ubuntu, pip upgrade lines are commented now. Now the install should run smoothly (tested on Ubuntu 18.04).

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