From e7a5bce8cc5c9c126767d4fe363e2b44589185c4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marek=20Wiewi=C3=B3rka?= Date: Sun, 23 Jul 2017 10:41:08 +0200 Subject: [PATCH 1/2] repo migration --- Jenkinsfile | 4 ++-- built.sbt | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/Jenkinsfile b/Jenkinsfile index e0cd8f2..79f2993 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -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" } } diff --git a/built.sbt b/built.sbt index d705cda..95ba4f1 100644 --- a/built.sbt +++ b/built.sbt @@ -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/" ) @@ -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 From 0d2594887740f0914604247918bea3d5503985b4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Wiktor=20Ku=C5=9Bmirek?= Date: Sun, 23 Jul 2017 16:33:13 +0200 Subject: [PATCH 2/2] repo migration in R code --- R/CNVCALLER.RUNNER/inst/run_cnvcaller.R | 4 ++-- R/tests/test_run_cnvcaller.R | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/CNVCALLER.RUNNER/inst/run_cnvcaller.R b/R/CNVCALLER.RUNNER/inst/run_cnvcaller.R index 0e84334..6b181ee 100755 --- a/R/CNVCALLER.RUNNER/inst/run_cnvcaller.R +++ b/R/CNVCALLER.RUNNER/inst/run_cnvcaller.R @@ -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") diff --git a/R/tests/test_run_cnvcaller.R b/R/tests/test_run_cnvcaller.R index 7c38047..89d7936 100644 --- a/R/tests/test_run_cnvcaller.R +++ b/R/tests/test_run_cnvcaller.R @@ -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")