From d32ee68d6295b36d77bd115b1fb0af2068f29837 Mon Sep 17 00:00:00 2001 From: Sasha Sherstnev Date: Mon, 14 Oct 2013 10:58:40 +0100 Subject: [PATCH] Define path to UNIREF database in conf/Executable.properties --- conf/Executable.properties | 8 +++++++- runner/compbio/runner/predictors/Jpred.java | 14 +++++++++----- webservices/compbio/ws/client/Jws2Client.java | 2 +- 3 files changed, 17 insertions(+), 7 deletions(-) diff --git a/conf/Executable.properties b/conf/Executable.properties index a4f1aa3..cbc8474 100644 --- a/conf/Executable.properties +++ b/conf/Executable.properties @@ -218,7 +218,13 @@ aacon.limits.file = conf/settings/AAConLimits.xml local.jpred.bin = binaries/src/jpred/jpred.pl #cluster.jpred.bin = /home/jabaws/binaries/src/jpred/jpred.pl # These paths will be converted to absolute if relative. -jpred.bin.env = BLASTMAT#binaries/src/jpred/data/blast;UNIREFDB#binaries/src/jpred/unirefdb; +jpred.bin.env = BLASTMAT#binaries/src/jpred/data/blast +# The varible jpred.data.uniref.path define a path to Uniref90 files used by Jpred. If +# you install the database to a different path chenge the variable here +jpred.data.uniref.path = /data/UNIREFdb +# WARNING!!! +# Redefine jpred.data.uniref.name if you do undestand what the variable means +jpred.data.uniref.name = cluster ### This parameters specifies the directory where the matrices files are stored jpred.presets.file = conf/settings/JpredPresets.xml jpred.parameters.file = conf/settings/JpredParameters.xml diff --git a/runner/compbio/runner/predictors/Jpred.java b/runner/compbio/runner/predictors/Jpred.java index 12f9487..0e08e0a 100644 --- a/runner/compbio/runner/predictors/Jpred.java +++ b/runner/compbio/runner/predictors/Jpred.java @@ -40,7 +40,8 @@ import compbio.metadata.ResultNotAvailableException; /** * Command line * - * jpred.pl -in d16vpa_.fas -outfile res_d16vpa_ -dbname ported_db -dbpath /data/UNIREFdb -ncpu 4 + * jpred.pl -in d16vpa_.fas -outfile res_d16vpa_ -dbname ported_db -dbpath + * /data/UNIREFdb -ncpu 4 * * @author asherstnev * @@ -59,15 +60,17 @@ public class Jpred extends SkeletalExecutable { public static final String STAT_FILE = "stat.txt"; public Jpred() { + String dbpath = ph.getProperty("jpred.data.uniref.path"); + String dbname = ph.getProperty("jpred.data.uniref.name"); addParameters(Arrays.asList("-logfile " + STAT_FILE)); - addParameters(Arrays.asList("-jabaws")); + addParameters(Arrays.asList("-dbpath " + dbpath)); + addParameters(Arrays.asList("-dbname " + dbname)); } // HashMap @SuppressWarnings("unchecked") @Override - public JpredAlignment getResults(String workDirectory) - throws ResultNotAvailableException { + public JpredAlignment getResults(String workDirectory) throws ResultNotAvailableException { JpredAlignment annotations = null; try { InputStream inStream = new FileInputStream(new File(workDirectory, getOutput())); @@ -129,7 +132,8 @@ public class Jpred extends SkeletalExecutable { @Override public CommandBuilder getParameters(ExecProvider provider) { - // If number of cores is provided, set it for the cluster execution only! + // If number of cores is provided, set it for the cluster execution + // only! if (provider == Executable.ExecProvider.Cluster) { int cpunum = SkeletalExecutable.getClusterCpuNum(getType()); cpunum = (cpunum == 0) ? 1 : cpunum; diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java index 095d8fd..daeb8fa 100644 --- a/webservices/compbio/ws/client/Jws2Client.java +++ b/webservices/compbio/ws/client/Jws2Client.java @@ -467,8 +467,8 @@ public class Jws2Client { jobId = msaws.align(fastalist); } System.out.println("\ncalling program........."); - long startTime = System.nanoTime(); /* + long startTime = System.nanoTime(); while (JobStatus.RUNNING == msaws.getJobStatus(jobId)) { Thread.sleep(1000); long endTime = System.nanoTime(); -- 1.7.10.2