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repo migration #54

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merged 3 commits into from
Aug 1, 2017
Merged

repo migration #54

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e7a5bce
repo migration
mwiewior Jul 23, 2017
0d25948
repo migration in R code
wk1993 Jul 23, 2017
65f74bc
Merge pull request #1 from wkusmirek/repo-migration
mwiewior Aug 1, 2017
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4 changes: 2 additions & 2 deletions Jenkinsfile
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Original file line number Diff line number Diff line change
Expand Up @@ -16,9 +16,9 @@ pipeline {
stage('Build R package') {
steps {
echo 'Building R package....'
sh "cd R && R CMD build CODEXCOV/ && curl -v --user ${NEXUS_USER}:${NEXUS_PASS} --upload-file CODEXCOV_0.0.1.tar.gz http://zsibio.ii.pw.edu.pl:50007/repository/r-zsibio/src/contrib/CODEXCOV_0.0.1.tar.gz"
sh "cd R && R CMD build CODEXCOV/ && curl -v --user ${NEXUS_USER}:${NEXUS_PASS} --upload-file CODEXCOV_0.0.1.tar.gz http://zsibio.ii.pw.edu.pl/nexus/repository/r-zsibio/src/contrib/CODEXCOV_0.0.1.tar.gz"

sh "cd R && R CMD build CNVCALLER.RUNNER/ && curl -v --user ${NEXUS_USER}:${NEXUS_PASS} --upload-file CNVCALLER.RUNNER_0.0.1.tar.gz http://zsibio.ii.pw.edu.pl:50007/repository/r-zsibio/src/contrib/CNVCALLER.RUNNER_0.0.1.tar.gz"
sh "cd R && R CMD build CNVCALLER.RUNNER/ && curl -v --user ${NEXUS_USER}:${NEXUS_PASS} --upload-file CNVCALLER.RUNNER_0.0.1.tar.gz http://zsibio.ii.pw.edu.pl/nexus/repository/r-zsibio/src/contrib/CNVCALLER.RUNNER_0.0.1.tar.gz"
}

}
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4 changes: 2 additions & 2 deletions R/CNVCALLER.RUNNER/inst/run_cnvcaller.R
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Expand Up @@ -91,13 +91,13 @@ run_caller <- function(parameters, cov_table){
}

if (!file.exists("zsi-bio-cdh-hive-jdbc_2.11-0.1-assembly.jar")) {
download.file("http://zsibio.ii.pw.edu.pl:50007/repository/maven-releases/pl/edu/pw/ii/zsibio/zsi-bio-cdh-hive-jdbc_2.11/0.1/zsi-bio-cdh-hive-jdbc_2.11-0.1-assembly.jar",destfile="zsi-bio-cdh-hive-jdbc_2.11-0.1-assembly.jar")
download.file("http://zsibio.ii.pw.edu.pl/nexus/repository/maven-releases/pl/edu/pw/ii/zsibio/zsi-bio-cdh-hive-jdbc_2.11/0.1/zsi-bio-cdh-hive-jdbc_2.11-0.1-assembly.jar",destfile="zsi-bio-cdh-hive-jdbc_2.11-0.1-assembly.jar")
}
drv_hive <- JDBC("com.cloudera.hiveserver2.hive.core.Hive2JDBCDriver", "./zsi-bio-cdh-hive-jdbc_2.11-0.1-assembly.jar",identifier.quote="`")
conn_hive <- dbConnect(drv_hive, "jdbc:hive2://cdh01.ii.pw.edu.pl:10000", "mwiewior", "")

if (!file.exists("postgresql-42.1.1.jar")) {
download.file("http://zsibio.ii.pw.edu.pl:50007/repository/zsi-bio-raw/common/jdbc/postgresql-42.1.1.jar",destfile="postgresql-42.1.1.jar")
download.file("http://zsibio.ii.pw.edu.pl/nexus/repository/zsi-bio-raw/common/jdbc/postgresql-42.1.1.jar",destfile="postgresql-42.1.1.jar")
}
drv_psql <- JDBC("org.postgresql.Driver", "./postgresql-42.1.1.jar",identifier.quote="`")
conn_psql <- dbConnect(drv_psql, "jdbc:postgresql://cdh00.ii.pw.edu.pl:15432/cnv-opt", "cnv-opt", "zsibio321")
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4 changes: 2 additions & 2 deletions R/tests/test_run_cnvcaller.R
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Expand Up @@ -6,12 +6,12 @@ library(RJDBC)

# make connections to database
if (!file.exists("zsi-bio-cdh-hive-jdbc_2.11-0.1-assembly.jar")) {
download.file("http://zsibio.ii.pw.edu.pl:50007/repository/maven-releases/pl/edu/pw/ii/zsibio/zsi-bio-cdh-hive-jdbc_2.11/0.1/zsi-bio-cdh-hive-jdbc_2.11-0.1-assembly.jar",destfile="zsi-bio-cdh-hive-jdbc_2.11-0.1-assembly.jar")
download.file("http://zsibio.ii.pw.edu.pl/nexus/repository/maven-releases/pl/edu/pw/ii/zsibio/zsi-bio-cdh-hive-jdbc_2.11/0.1/zsi-bio-cdh-hive-jdbc_2.11-0.1-assembly.jar",destfile="zsi-bio-cdh-hive-jdbc_2.11-0.1-assembly.jar")
}
drv_hive <- JDBC("com.cloudera.hiveserver2.hive.core.Hive2JDBCDriver", "./zsi-bio-cdh-hive-jdbc_2.11-0.1-assembly.jar",identifier.quote="`")
conn_hive <- dbConnect(drv_hive, "jdbc:hive2://cdh01.ii.pw.edu.pl:10000", "mwiewior", "")
if (!file.exists("postgresql-42.1.1.jar")) {
download.file("http://zsibio.ii.pw.edu.pl:50007/repository/zsi-bio-raw/common/jdbc/postgresql-42.1.1.jar",destfile="postgresql-42.1.1.jar")
download.file("http://zsibio.ii.pw.edu.pl/nexus/repository/zsi-bio-raw/common/jdbc/postgresql-42.1.1.jar",destfile="postgresql-42.1.1.jar")
}
drv_psql <- JDBC("org.postgresql.Driver", "./postgresql-42.1.1.jar",identifier.quote="`")
conn_psql <- dbConnect(drv_psql, "jdbc:postgresql://cdh00.ii.pw.edu.pl:15432/cnv-opt", "cnv-opt", "zsibio321")
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4 changes: 2 additions & 2 deletions built.sbt
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Expand Up @@ -51,7 +51,7 @@ libraryDependencies ++= Seq(

resolvers ++= Seq(
"Job Server Bintray" at "https://dl.bintray.com/spark-jobserver/maven",
"zsibio-snapshots" at "http://zsibio.ii.pw.edu.pl:50007/repository/maven-snapshots/",
"zsibio-snapshots" at "http://zsibio.ii.pw.edu.pl/nexus/repository/maven-snapshots/",
"spring" at "http://repo.spring.io/libs-milestone/"
)

Expand Down Expand Up @@ -117,7 +117,7 @@ assemblyMergeStrategy in assembly := {

credentials += Credentials(Path.userHome / ".ivy2" / ".credentials")
publishTo := {
val nexus = "http://zsibio.ii.pw.edu.pl:50007/repository/"
val nexus = "http://zsibio.ii.pw.edu.pl/nexus/repository/"
if (isSnapshot.value)
Some("snapshots" at nexus + "maven-snapshots")
else
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