ANTS with source needs little update

[Brainarea]

I was trying to install ANTS through sources and it was giving me the following error: "The unauthenticated git protocol on port 9418 is no longer supported"

I found out that git requires a change in the default url and this is easily done with a git config command.

This is the code that works for me for installing ANTS with source:

ENV ANTSPATH="/opt/ants-latest/bin"
PATH="/opt/ants-latest/bin:$PATH"
LD_LIBRARY_PATH="/opt/ants-latest/lib:$LD_LIBRARY_PATH" RUN apt-get update -qq
&& apt-get install -y -q --no-install-recommends
cmake
g++
gcc
git
make
zlib1g-dev
&& apt-get clean
&& rm -rf /var/lib/apt/lists/*
&& mkdir -p /tmp/ants/build
&& git config --global url."https://".insteadOf git://
&& git clone https://github.com/ANTsX/ANTs.git /tmp/ants/source
&& cd /tmp/ants/build
&& cmake -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF /tmp/ants/source
&& make -j1
&& mkdir -p /opt/ants-latest
&& mv bin lib /opt/ants-latest/
&& mv /tmp/ants/source/Scripts/* /opt/ants-latest/bin
&& rm -rf /tmp/ants

Hope this helps!

[kaczmarj]

thanks @Brainarea ! so the change would be to add

git config --global url."https://".insteadOf git://

to the source instructions?

[Brainarea]

thanks @Brainarea ! so the change would be to add

git config --global url."https://".insteadOf git://

to the source instructions?

Correct!

[github-actions[bot]]

This issue is stale because it has been open for 30 days with no activity.

[github-actions[bot]]

This issue was closed because it has been inactive for 14 days since being marked as stale.

[Remi-Gau]

Still valid but for a different reason.

Copy from run: https://github.com/ReproNim/neurodocker/actions/runs/6713805023/job/18246021919

Seems that it is not on our side though. Would have to dig into the install doc of ANTs.

#5 33.94 [  5%] Creating directories for 'ITKv5'
#5 34.02 [ 11%] Performing download step (git clone) for 'ITKv5'
#5 34.04 Cloning into 'ITKv5'...
#5 164.1 fatal: unable to connect to github.com:
#5 164.1 github.com[0: 140.82.113.3]: errno=Connection timed out
#5 164.1 
#5 164.1 Cloning into 'ITKv5'...
#5 295.1 fatal: unable to connect to github.com:
#5 295.1 github.com[0: 140.82.114.4]: errno=Connection timed out
#5 295.1 
#5 295.1 Cloning into 'ITKv5'...
#5 426.2 fatal: unable to connect to github.com:
#5 426.2 github.com[0: 140.82.113.4]: errno=Connection timed out
#5 426.2 
#5 426.2 CMake Error at ITKv5-prefix/tmp/ITKv5-gitclone.cmake:31 (message):
#5 426.2   Failed to clone repository:
#5 426.2   'git://github.com/InsightSoftwareConsortium/ITK.git'
#5 426.2 
#5 426.2 
#5 426.2 -- Had to git clone more than once:
#5 426.2           3 times.
#5 426.2 make[2]: *** [CMakeFiles/ITKv5.dir/build.make:98: ITKv5-prefix/src/ITKv5-stamp/ITKv5-download] Error 1
#5 426.2 make[1]: *** [CMakeFiles/Makefile2:85: CMakeFiles/ITKv5.dir/all] Error 2
#5 426.2 make: *** [Makefile:121: all] Error 2
#5 ERROR: process "/bin/sh -c apt-get update -qq     && apt-get install -y -q --no-install-recommends            ca-certificates            cmake            g++            gcc            git            make            zlib1g-dev     && rm -rf /var/lib/apt/lists/*     && mkdir -p /tmp/ants/build     && git clone https://github.com/ANTsX/ANTs.git /tmp/ants/source     && cd /tmp/ants/source     && git fetch --tags     && git -c advice.detachedHead=false checkout v2.3.0     && cd /tmp/ants/build     && cmake -DCMAKE_INSTALL_PREFIX=/opt/ants-2.3.0 -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF /tmp/ants/source     && make -j1     && mkdir -p /opt/ants-2.3.0     && if [ -d ANTS-build ]; then          cd ANTS-build          && make install          && mv ../../source/Scripts/ /opt/ants-2.3.0;        else          mv bin lib /opt/ants-2.3.0/          mv ../Scripts/* /opt/ants-2.3.0 ;     fi     && rm -rf /tmp/ants" did not complete successfully: exit code: 2
------
 > [2/3] RUN apt-get update -qq     && apt-get install -y -q --no-install-recommends            ca-certificates            cmake            g++            gcc            git            make            zlib1g-dev     && rm -rf /var/lib/apt/lists/*     && mkdir -p /tmp/ants/build     && git clone https://github.com/ANTsX/ANTs.git /tmp/ants/source     && cd /tmp/ants/source     && git fetch --tags     && git -c advice.detachedHead=false checkout v2.3.0     && cd /tmp/ants/build     && cmake -DCMAKE_INSTALL_PREFIX=/opt/ants-2.3.0 -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF /tmp/ants/source     && make -j1     && mkdir -p /opt/ants-2.3.0     && if [ -d ANTS-build ]; then          cd ANTS-build          && make install          && mv ../../source/Scripts/ /opt/ants-2.3.0;        else          mv bin lib /opt/ants-2.3.0/          mv ../Scripts/* /opt/ants-2.3.0 ;     fi     && rm -rf /tmp/ants:
426.2 CMake Error at ITKv5-prefix/tmp/ITKv5-gitclone.cmake:31 (message):
426.2   Failed to clone repository:
426.2   'git://github.com/InsightSoftwareConsortium/ITK.git'
426.2 
426.2 
426.2 -- Had to git clone more than once:
426.2           3 times.
426.2 make[2]: *** [CMakeFiles/ITKv5.dir/build.make:98: ITKv5-prefix/src/ITKv5-stamp/ITKv5-download] Error 1
426.2 make[1]: *** [CMakeFiles/Makefile2:85: CMakeFiles/ITKv5.dir/all] Error 2
426.2 make: *** [Makefile:121: all] Error 2