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bonsai-team / matam

Mapping-Assisted Targeted-Assembly for Metagenomics
GNU Affero General Public License v3.0
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preferred installation method #27

Closed rchikhi closed 5 years ago

rchikhi commented 7 years ago

I recall Pierre saying that Conda was the preferred method for getting MATAM, yet the README appears to recommend doing source compilation.

Also these "sudo apt-get" for a "quick installation" aren't user friendly, not so many users are root on their machine.

loic-couderc commented 7 years ago

From https://github.com/bonsai-team/matam#getting-started:

The recommended way of getting MATAM is through conda (see below)

In all cases, we have to rethink the README. The amount of info can be confusing.

ycl6 commented 6 years ago

The "Source code (zip/tar.gz)" provided in the releases page lacks the submodule contents, so does using git clone https://github.com/bonsai-team/matam.git

To download the complete source code (including submodules) for compilation, use git clone --recursive https://github.com/bonsai-team/matam.git

ppericard commented 6 years ago

The "Source code (zip/tar.gz)" provided in the releases page lacks the submodule contents

Yes, this is a feature lacking in GitHub. This is why we are not recommending getting MATAM source code this way.

so does using git clone https://github.com/bonsai-team/matam.git

In fact, this is not a problem. If you do not use the --recursive option when cloning the repository, the submodules will be recovered by running the build.py script to compile MATAM.