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Merge pull request #117 from veg/develop
Updating GARD to latest version of HyPhy. Updating all methods to use kwargs.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,94 @@ | ||
| var config = require("../../config.json"), | ||
| hyphyJob = require("../hyphyjob.js").hyphyJob, | ||
| code = require("../code").code, | ||
| util = require("util"), | ||
| fs = require("fs"), | ||
| path = require("path"); | ||
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| var cfel = function(socket, stream, params) { | ||
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| var self = this; | ||
| self.socket = socket; | ||
| self.stream = stream; | ||
| self.params = params; | ||
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| fs.writeFile('./cfel_params.json', JSON.stringify(self.params), function(err) { | ||
| if (err) throw err; | ||
| }); | ||
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| // object specific attributes | ||
| self.type = "cfel"; | ||
| self.qsub_script_name = "cfel.sh"; | ||
| self.qsub_script = __dirname + "/" + self.qsub_script_name; | ||
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| // parameter attributes | ||
| self.msaid = self.params.msa._id; | ||
| self.id = self.params.analysis._id; | ||
| self.genetic_code = code[self.params.msa[0].gencodeid + 1]; | ||
| self.nwk_tree = self.params.analysis.tagged_nwk_tree; | ||
| self.branch_sets = self.params.analysis.branch_sets.join(":"); | ||
| self.rate_variation = self.params.analysis.ds_variation == 1 ? "Yes" : "No"; | ||
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| // parameter-derived attributes | ||
| self.fn = __dirname + "/output/" + self.id; | ||
| self.output_dir = path.dirname(self.fn); | ||
| self.status_fn = self.fn + ".status"; | ||
| self.results_short_fn = self.fn + ".cfel"; | ||
| self.results_fn = self.fn + ".FEL.json"; | ||
| self.progress_fn = self.fn + ".cfel.progress"; | ||
| self.tree_fn = self.fn + ".tre"; | ||
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| self.qsub_params = [ | ||
| "-l walltime=" + | ||
| config.cfel_walltime + | ||
| ",nodes=1:ppn=" + | ||
| config.cfel_procs, | ||
| "-q", | ||
| config.qsub_avx_queue, | ||
| "-v", | ||
| "fn=" + | ||
| self.fn + | ||
| ",tree_fn=" + | ||
| self.tree_fn + | ||
| ",sfn=" + | ||
| self.status_fn + | ||
| ",pfn=" + | ||
| self.progress_fn + | ||
| ",rfn=" + | ||
| self.results_short_fn + | ||
| ",treemode=" + | ||
| self.treemode + | ||
| ",genetic_code=" + | ||
| self.genetic_code + | ||
| ",analysis_type=" + | ||
| self.type + | ||
| ",branch_sets=" + | ||
| self.branch_sets + | ||
| ",rate_variation=" + | ||
| self.rate_variation + | ||
| ",cwd=" + | ||
| __dirname + | ||
| ",msaid=" + | ||
| self.msaid + | ||
| ",procs=" + | ||
| config.cfel_procs, | ||
| "-o", | ||
| self.output_dir, | ||
| "-e", | ||
| self.output_dir, | ||
| self.qsub_script | ||
| ]; | ||
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| // Write tree to a file | ||
| fs.writeFile(self.tree_fn, self.nwk_tree, function(err) { | ||
| if (err) throw err; | ||
| }); | ||
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| // Ensure the progress file exists | ||
| fs.openSync(self.progress_fn, "w"); | ||
| self.init(); | ||
| }; | ||
|
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| util.inherits(cfel, hyphyJob); | ||
| exports.cfel = cfel; |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| #!/bin/bash | ||
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| export PATH=/usr/local/bin:$PATH | ||
| source /etc/profile.d/modules.sh | ||
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| module load aocc/1.3.0 | ||
| module load openmpi/gnu/3.0.2 | ||
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| FN=$fn | ||
| CWD=$cwd | ||
| TREE_FN=$tree_fn | ||
| STATUS_FILE=$sfn | ||
| PROGRESS_FILE=$pfn | ||
| RESULTS_FN=$rfn | ||
| GENETIC_CODE=$genetic_code | ||
| RATE_VARIATION=$rate_variation | ||
| PROCS=$procs | ||
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| sets=(`echo $branch_sets | sed 's/:/\n/g'`) | ||
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| BRANCH_SETS=$(for x in ${sets[@]}; do echo -n " --branch-set $x "; done;) | ||
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| HYPHY=$CWD/../../.hyphy/HYPHYMPI | ||
| HYPHY_PATH=$CWD/../../.hyphy/res/ | ||
| RESULTS_FILE=$fn.FEL.json | ||
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| export HYPHY_PATH=$HYPHY_PATH | ||
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| trap 'echo "Error" > $STATUS_FILE; exit 1' ERR | ||
| echo "mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH contrast-fel --alignment $FN --tree $TREE_FN $BRANCH_SETS --output $RESULTS_FILE >> $PROGRESS_FILE" | ||
| mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH contrast-fel --alignment $FN --tree $TREE_FN $BRANCH_SETS --output $RESULTS_FILE >> $PROGRESS_FILE | ||
| echo "Completed" > $STATUS_FILE | ||
|
|
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