changelog + make-targz

ablab · Jul 22, 2016 · 8ccafb3 · 8ccafb3
1 parent fd6ffb4
commit 8ccafb3
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Showing 4 changed files with 15 additions and 12 deletions.
diff --git a/assembler/changelog.html b/assembler/changelog.html
@@ -5,7 +5,11 @@ <h2>SPAdes Genome Assembler changelog</h2>
 
 <h3>SPAdes 3.9.0, 23 July 2016</h3>
 
-NEW: rnaSPAdes pipeline for de novo transcriptome assembly from RNA-Seq data.
+<p>NEW: rnaSPAdes pipeline for de novo transcriptome assembly from RNA-Seq data.</p>
+
+<p>CHANGE: Improved memory consumption in metagenomic pipeline.</p>
+
+<p>FIX: Several minor bugs.</p>
 
 <h3>SPAdes 3.8.2, 10 July 2016</h3>
 

diff --git a/assembler/src/CMakeLists.txt b/assembler/src/CMakeLists.txt
@@ -129,6 +129,9 @@ install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/../dipspades_manual.html"
 install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/../truspades_manual.html"
         DESTINATION share/spades
         COMPONENT runtime)
+install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/../rnaspades_manual.html"
+        DESTINATION share/spades
+        COMPONENT runtime)
 install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/../LICENSE"
         DESTINATION share/spades
         COMPONENT runtime)

diff --git a/assembler/src/tools/spades_holybox_compile.sh b/assembler/src/tools/spades_holybox_compile.sh
@@ -2,7 +2,7 @@
 
 # Script for compiling SPAdes using holy build box
 # To compile spades run
-# docker run -t -i -v <path with algorithmic-biology repository>:/gitrep --rm phusion/holy-build-box-64:latest  bash /gitrep/algorithmic-biology/assembler/src/tools/spades_holybox_compile.sh
+# docker run -t -i -v <path to spades_compile.sh>:/spades/ --rm phusion/holy-build-box-64:latest  bash /spades/src/tools/spades_holybox_compile.sh
 
 set -e
 source /hbb_exe/activate
@@ -11,7 +11,7 @@ set -x
 
 yum install bzip2-devel
 
-cd /gitrep/algorithmic-biology/assembler
+cd /spades
 ./spades_compile.sh -DSPADES_STATIC_BUILD=1
 
 cd build_spades

diff --git a/make-targz.sh b/make-targz.sh
@@ -4,15 +4,11 @@ rm -rf $TARGET_DIR
 SRC_DIR=$TARGET_DIR/src
 mkdir -p $SRC_DIR
 
-cp -r assembler/src/debruijn $SRC_DIR/
-cp -r assembler/src/hammer $SRC_DIR/
-cp -r assembler/src/dipspades $SRC_DIR/
-cp -r assembler/src/ionhammer $SRC_DIR/
-cp -r assembler/src/scaffold_correction $SRC_DIR/
+cp -r assembler/src/modules $SRC_DIR/
+cp -r assembler/src/utils $SRC_DIR/
+cp -r assembler/src/projects $SRC_DIR/
 cp -r assembler/src/include $SRC_DIR/
-cp -r assembler/src/io $SRC_DIR/
 cp -r assembler/src/cmake $SRC_DIR/
-cp -r assembler/src/corrector $SRC_DIR/
 cp -r assembler/src/spades_pipeline $SRC_DIR/
 cp assembler/src/CMakeLists.txt $SRC_DIR/
 
@@ -34,6 +30,8 @@ cp assembler/README $TARGET_DIR/
 cp assembler/VERSION $TARGET_DIR/
 cp assembler/spades.py $TARGET_DIR/
 cp assembler/rnaspades.py $TARGET_DIR/
+cp assembler/metaspades.py $TARGET_DIR/
+cp assembler/plasmidspades.py $TARGET_DIR/
 cp assembler/dipspades.py $TARGET_DIR/
 cp assembler/truspades.py $TARGET_DIR/
 cp assembler/spades_compile.sh $TARGET_DIR/
@@ -49,8 +47,6 @@ cd $TARGET_DIR/
 touch src/CMakeListsInternal.txt
 rm -r configs/debruijn/datasets_archive
 rm -r configs/debruijn/datasets
-rm  configs/debruijn/datasets*
-rm  configs/debruijn/deprecated*
 find . -name ".?*" | xargs rm -r
 
 cd ..