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Fix incompatibilities with Python 3+ and improve installation instructions in the README #22

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Fix incompatibilities with Python 3+ and improve installation instructions in the README #22

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7776982
fix: run.py formatting and shebang
AlexSartori May 23, 2025
cb377c5
fix: OGDF/makeMakefile.py syntax errors on python3
AlexSartori May 23, 2025
5642793
feat: correct installation instructions in README.md
AlexSartori May 23, 2025
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6 changes: 2 additions & 4 deletions OGDF/makeMakefile.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# Make Makefile
#
# October 2012
Expand Down Expand Up @@ -278,7 +278,7 @@ def Walk(curdir):
for v in versions:
# print target&depend: add full path spec, incl. version & ignore extra line
path = v.call() + '/' +fullname[:-len(name)]
makefile.write(path + targetAndDepend[:-1] + '\n')
makefile.write(path + targetAndDepend[:-1].decode("utf-8") + '\n')

# ensure folder
makefile.write('\t$(MKDIR) ' + v.call() + '/' + fullname[:-len(name)-1] + '\n')
Expand Down Expand Up @@ -469,5 +469,3 @@ def InstallHeaders(curdir, makefile, installPrefix):
makefile.close()

print('Makefile generated')


19 changes: 17 additions & 2 deletions README.md
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Expand Up @@ -4,10 +4,25 @@ MetaCarvel is an updated version of previous metagenome scaffolder Bambus 2. To

You can install Networkx as described [here](https://pypi.org/project/networkx/).
MetCarvel can work with the latest NetworkX version 2.5
Briefly, you need to run following:
```

Briefly, you need to run the following:
```bash
# Install pip dependencies (ensure you also have samtools and bedtools installed)
pip install numpy (tested with version 1.20)
pip install networkx>=2.5

# Clone the repository
git clone https://github.com/marbl/MetaCarvel
cd MetaCarvel/
git submodule init
git submodule update --recursive

# Build OGDF
cd OGDF/
python makeMakefile.py
make
cd ..
make
```

## The detailed documentation and tutorial to install and run MetaCarvel can be found on [Wiki](https://github.com/marbl/MetaCarvel/wiki).
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