719dedcf737aa6db81f06c167998e70531ac804b
examples/embuild.md
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4 | 4 | http://huanglab.phys.hust.edu.cn/EMBuild/ |
5 | 5 | |
6 | 6 | |
7 | - |
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8 | -**STRIDE must be installed by user** |
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9 | - |
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10 | -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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11 | - |
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12 | - |
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13 | 7 | ``` |
8 | + |
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14 | 9 | #!/usr/bin/env bash |
15 | 10 | |
16 | 11 | ## SBGrid EMBuild example - EMD-0346 |
... | ... | @@ -38,20 +33,6 @@ ACKNOWLEDGE |
38 | 33 | #SBATCH --job-name=JV-embuild |
39 | 34 | |
40 | 35 | |
41 | -# STRIDE dependency must be downloaded/installed by user |
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42 | -curl -kLO http://webclu.bio.wzw.tum.de/stride/stride.tar.gz |
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43 | -# Untars in current directory - make a subdir first |
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44 | -mkdir stride |
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45 | -mv stride.tar.gz stride |
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46 | -cd stride |
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47 | -tar zxf stride.tar.gz |
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48 | -make |
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49 | -# Absolute stride path required in call to EMBuild |
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50 | -stride_path=`pwd`/stride |
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51 | -echo "STRIDE path: ${stride_path} " |
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52 | -cd .. |
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53 | - |
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54 | - |
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55 | 36 | # Load cuda |
56 | 37 | module load cuda/11.2 |
57 | 38 | |
... | ... | @@ -84,7 +65,11 @@ EMBuild 0346_MC.mrc init_chains.pdb 4.0 6N52_EMBuild.pdb |
84 | 65 | |
85 | 66 | rearrangepdb 6N52_EMBuild.pdb 6N52_EMBuild_rearranged.pdb |
86 | 67 | |
68 | +stride_path=/programs//x86_64-linux//stride/20170124/bin.capsules/stride |
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87 | 69 | EMBuild 0346_MC.mrc 6N52_EMBuild_rearranged.pdb 4.0 6N52_EMBuild_scored.pdb \ |
88 | 70 | --score -stride ${stride_path} |
71 | + |
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72 | + |
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73 | + |
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89 | 74 | |
90 | 75 | ``` |
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