rbbt-util 5.25.14 → 5.25.15

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: e5aabac2c8c621d8ee26f59822fdb44044de2150
-  data.tar.gz: 2bc06d77e9770da322089b495807c7b9478dcd19
+  metadata.gz: 84ee8220e10055644029255ec78f3650d9cbb43c
+  data.tar.gz: 7709e99accf8b271dd67b684643490f29b629aa6
 SHA512:
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-  data.tar.gz: b601014d631449cfd2363461f9aa83f590fc4998ecd14ddc0fb4f21d7b6577e6015c9b33f15e57881dc82d8c7c94d241665723c46246db79c674c105e3aee9b0
+  metadata.gz: 6d9b3a82a19ddf6a305816aa0c1c74c5bb4c25285fa229defb0dc7f3d6c03a95302f594d132123b33e7fa2fe800f630015173fcb86f0ce8d76e72fab703de5d7
+  data.tar.gz: 189622da3a2235075c903abe9d6a06ec2f307697083b8626e1ed35c34c2a22b0f7a6d9ee3786bb2f54d8e3f996e901dd78a1424490f0f1fde3e2f965529a74c4

data/lib/rbbt/hpc.rb

@@ -263,7 +263,8 @@ EOF
         if File.exists?(fout)
           return
         elsif dry_run
-          STDERR.puts Log.color(:magenta, "To execute run: sbatch '#{workdir}/command.slurm'")
+          STDERR.puts Log.color(:magenta, "To execute run: ") + Log.color(:blue, "sbatch '#{workdir}/command.slurm'")
+          STDERR.puts Log.color(:magenta, "To monitor progress run (needs local rbbt): ") + Log.color(:blue, "rbbt mn --tail -w '#{workdir}'")
           raise Marenostrum::SBATCH, workdir
         else
           Open.rm fsync

data/lib/rbbt/resource/util.rb

@@ -33,6 +33,7 @@ module Resource
   def set_software_env(software_dir)
     software_dir.find_all.each do |software_dir|
       next unless software_dir.exists?
+      software_dir = File.expand_path(software_dir)
       bin_dir = File.join(software_dir, 'bin')
       opt_dir = File.join(software_dir, 'opt')
 
@@ -50,28 +51,40 @@ module Resource
       end
 
       Open.read(File.join opt_dir, '.c-paths').split(/\n/).each do |line|
-        Misc.env_add('C_INCLULDE_PATH',line.chomp)
+        dir = line.chomp
+        dir = File.join(opt_dir, dir) unless dir[0] == "/"
+        Misc.env_add('C_INCLULDE_PATH',dir)
       end if File.exist? File.join(opt_dir, '.c-paths')
 
       Open.read(File.join opt_dir, '.ld-paths').split(/\n/).each do |line|
-        Misc.env_add('LD_LIBRARY_PATH',line.chomp)
-        Misc.env_add('LD_RUN_PATH',line.chomp)
+        dir = line.chomp
+        dir = File.join(opt_dir, dir) unless dir[0] == "/"
+        Misc.env_add('LD_LIBRARY_PATH',dir)
+        Misc.env_add('LD_RUN_PATH',dir)
       end if File.exist? File.join(opt_dir, '.ld-paths')
 
       Open.read(File.join opt_dir, '.pkgconfig-paths').split(/\n/).each do |line|
-        Misc.env_add('PKG_CONFIG_PATH',line.chomp)
+        dir = line.chomp
+        dir = File.join(opt_dir, dir) unless dir[0] == "/"
+        Misc.env_add('PKG_CONFIG_PATH',dir)
       end if File.exist? File.join(opt_dir, '.pkgconfig-paths')
 
       Open.read(File.join opt_dir, '.aclocal-paths').split(/\n/).each do |line|
-        Misc.env_add('ACLOCAL_FLAGS', "-I#{File.join(opt_dir, line.chomp)}", ' ')
+        dir = line.chomp
+        dir = File.join(opt_dir, dir) unless dir[0] == "/"
+        Misc.env_add('ACLOCAL_FLAGS', "-I #{dir}", ' ')
       end if File.exist? File.join(opt_dir, '.aclocal-paths')
 
       Open.read(File.join opt_dir, '.java-classpaths').split(/\n/).each do |line|
-        Misc.env_add('CLASSPATH', "#{File.join(opt_dir,'java', 'lib', line.chomp)}")
+        dir = line.chomp
+        dir = File.join(opt_dir, dir) unless dir[0] == "/"
+        Misc.env_add('CLASSPATH', "#{dir}")
       end if File.exist? File.join(opt_dir, '.java-classpaths')
 
       Dir.glob(File.join opt_dir, 'jars', '*').each do |file|
-        Misc.env_add('CLASSPATH', "#{File.expand_path(file)}")
+        dir = line.chomp
+        dir = File.join(opt_dir, dir) unless dir[0] == "/"
+        Misc.env_add('CLASSPATH', "#{dir}")
       end
 
       if File.exist?(File.join(opt_dir, '.post_install')) and File.directory?(File.join(opt_dir, '.post_install'))

data/share/install/software/lib/install_helpers

@@ -31,7 +31,8 @@ function add2file(){
     file=$1
     line=$2
 
-    grep "$2" "$1" || echo "$2" >> "$1"
+    rel=$(realpath --relative-to=$OPT_DIR $rel)
+    grep "$rel" "$file" || echo "$rel" >> "$file"
 }
 
 #{{{ GET PKG OPT_BUILD_DIR

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.25.14
+  version: 5.25.15
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-01-08 00:00:00.000000000 Z
+date: 2019-01-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -333,7 +333,6 @@ files:
 - share/color/color_names
 - share/color/diverging_colors.hex
 - share/config.ru
-- share/install/software/HTSLIB
 - share/install/software/lib/install_helpers
 - share/rbbt_commands/alias
 - share/rbbt_commands/app/install

data/share/install/software/HTSLIB

@@ -1,6 +0,0 @@
-#!/bin/bash
-
-name='htslib'
-url="https://github.com/samtools/htslib/releases/download/1.3/htslib-1.3.tar.bz2"
-
-install_src "$name" "$url"