examples/embuild.md
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@@ -4,13 +4,8 @@
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http://huanglab.phys.hust.edu.cn/EMBuild/
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-
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-**STRIDE must be installed by user**
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-
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-The STRIDE program needed by EMBuild cannot be distributed with SBGrid. Users must download this themselves. An example is provided in the script below.
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-
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-
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```
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+
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#!/usr/bin/env bash
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## SBGrid EMBuild example - EMD-0346
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@@ -38,20 +33,6 @@ ACKNOWLEDGE
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#SBATCH --job-name=JV-embuild
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-# STRIDE dependency must be downloaded/installed by user
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-curl -kLO http://webclu.bio.wzw.tum.de/stride/stride.tar.gz
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-# Untars in current directory - make a subdir first
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-mkdir stride
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-mv stride.tar.gz stride
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-cd stride
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-tar zxf stride.tar.gz
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-make
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-# Absolute stride path required in call to EMBuild
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-stride_path=`pwd`/stride
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-echo "STRIDE path: ${stride_path} "
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-cd ..
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-
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-
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# Load cuda
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module load cuda/11.2
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@@ -84,7 +65,11 @@ EMBuild 0346_MC.mrc init_chains.pdb 4.0 6N52_EMBuild.pdb
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rearrangepdb 6N52_EMBuild.pdb 6N52_EMBuild_rearranged.pdb
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+stride_path=/programs//x86_64-linux//stride/20170124/bin.capsules/stride
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EMBuild 0346_MC.mrc 6N52_EMBuild_rearranged.pdb 4.0 6N52_EMBuild_scored.pdb \
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--score -stride ${stride_path}
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+
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+
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+
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```
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\ No newline at end of file