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Remove
local.json
in favor of system variables (#19)
* remove local.json * refactor to use third party binaries as system variables * add THIRDPARTY.md * update dockerfile * update tests
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# Installation of Third-Party dependencies | ||
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These instructions assuming you are installing locally in a Ubuntu Linux system, different steps may be required for other systems. | ||
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All will be installed in a `software` directory in your `$HOME` directory. | ||
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## System dependendencies | ||
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```bash | ||
$ sudo apt-get update && \ | ||
sudo apt-get install -y build-essential libboost-all-dev | ||
``` | ||
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## Muscle | ||
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```bash | ||
$ mkdir -p $HOME/software && cd $HOME/software | ||
$ mkdir muscle3.8.1551 && cd muscle3.8.1551 | ||
$ wget https://drive5.com/muscle/muscle_src_3.8.1551.tar.gz | ||
$ tar -zxf muscle_src_3.8.1551.tar.gz && rm muscle_src_3.8.1551.tar.gz | ||
$ make | ||
$ export MUSCLE_BIN=$HOME/software/muscle3.8.1551/muscle | ||
``` | ||
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## Freesasa | ||
```bash | ||
$ mkdir -p $HOME/software && cd $HOME/software | ||
$ wget https://github.com/mittinatten/freesasa/releases/download/2.0.3/freesasa-2.0.3.tar.gz | ||
$ tar -zxf freesasa-2.0.3.tar.gz && rm freesasa-2.0.3.tar.gz | ||
$ cd freesasa-2.0.3 | ||
$ ./configure --disable-json --prefix=`pwd` | ||
$ make | ||
$ make install | ||
$ export FREESASA_BIN=$HOME/software/freesasa-2.0.3/bin/freesasa | ||
``` | ||
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## HSSPCONV | ||
```bash | ||
$ mkdir -p $HOME/software && cd $HOME/software | ||
$ wget https://github.com/cmbi/hssp/archive/3.1.5.tar.gz | ||
$ tar -zxf 3.1.5.tar.gz && rm 3.1.5.tar.gz | ||
$ cd hssp-3.1.5 | ||
$ ./autogen.she | ||
$ ./configure | ||
$ make hsspconv | ||
$ export HSSPCONV_BIN=$HOME/software/hssp-3.1.5/hsspconv | ||
``` | ||
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## Protdist | ||
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Protdist is distributed together with WHISCY, you can find it in the `whiscy` directory. We are working on a better way to install this dependency 🙂 | ||
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```bash | ||
$ mkdir -p $HOME/software && cd $HOME/software | ||
$ git clone https://github.com/haddocking/whiscy | ||
$ mv whiscy/bin/protdist . && rm -rf whiscy | ||
$ cd protdist | ||
$ bash compile.sh | ||
$ export PROTDIST_BIN=$HOME/software/protdist/protdist | ||
``` | ||
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--- | ||
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In the end the system variables that define the third-party dependencies should look like this: | ||
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```bash | ||
export MUSCLE_BIN=$HOME/software/muscle3.8.1551/muscle | ||
export FREESASA_BIN=$HOME/software/freesasa-2.0.3/bin/freesasa | ||
export HSSPCONV_BIN=$HOME/software/hssp-3.1.5/hsspconv | ||
export PROTDIST_BIN=$HOME/software/protdist/protdist | ||
``` |
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import os | ||
from pathlib import Path | ||
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MUSCLE_BIN = os.environ.get("MUSCLE_BIN") | ||
FREESASA_BIN = os.environ.get("FREESASA_BIN") | ||
HSSPCONV_BIN = os.environ.get("HSSPCONV_BIN") | ||
PROTDIST_BIN = os.environ.get("PROTDIST_BIN") | ||
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# Make sure none of them are None | ||
if MUSCLE_BIN is None: | ||
raise ValueError("MUSCLE_BIN not found in system variables") | ||
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if FREESASA_BIN is None: | ||
raise ValueError("FREESASA_BIN not found in system variables") | ||
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if HSSPCONV_BIN is None: | ||
raise ValueError("HSSPCONV_BIN not found in system variables") | ||
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if PROTDIST_BIN is None: | ||
raise ValueError("PROTDIST_BIN not found in system variables") | ||
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PARAM_PATH = Path(Path(__file__).parent.parent, "param") | ||
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CUTOFF = { | ||
"sa_pred_cutoff": 15.0, | ||
"sa_act_cutoff": 40.0, | ||
"air_cutoff": 0.18, | ||
"air_dist_cutoff": 6.5, | ||
} | ||
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AIR = { | ||
"air_pro_percentage": 10.0, | ||
"air_wm_pro_or": 98.52, | ||
"air_wm_whis_or": 0.370515, | ||
"air_wm_pro_and": 55.42, | ||
"air_wm_whis_and": 0.106667, | ||
} |
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