add minimap2 v2.24.0

cokelaer · Apr 11, 2023 · f2e742e · f2e742e
1 parent a6b09b8
commit f2e742e
Show file tree

Hide file tree

Showing 2 changed files with 40 additions and 0 deletions.
diff --git a/damona/software/minimap2/Singularity.minimap2_2.24.0 b/damona/software/minimap2/Singularity.minimap2_2.24.0
@@ -0,0 +1,18 @@
+Bootstrap: docker
+From: alpine:3.17
+
+%labels
+  Author Sequana Team
+
+%post
+  MINIMAP2_VERSION=2.24
+
+  apk update && apk upgrade && apk add bash libc6-compat curl
+
+  curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VERSION}/minimap2-${MINIMAP2_VERSION}_x64-linux.tar.bz2 | tar -jxf - minimap2-${MINIMAP2_VERSION}_x64-linux/minimap2 \
+    && mv ./minimap2-${MINIMAP2_VERSION}_x64-linux/minimap2 /usr/local/bin
+
+  apk del curl
+
+%runscript
+  exec minimap2 "$@"
diff --git a/damona/software/samtools_minimap2/Singularity.samtools_1.17_minimap2_2.24.0 b/damona/software/samtools_minimap2/Singularity.samtools_1.17_minimap2_2.24.0
@@ -0,0 +1,22 @@
+Bootstrap: docker
+From: alpine:3.17
+
+%labels
+  Author Sequana Team
+
+%post
+  SAMTOOLS_VERSION=1.17
+  MINIMAP2_VERSION=2.24
+
+  apk update && apk upgrade && apk add bash libc6-compat curl
+  # samtools deps
+  apk add autoconf automake make gcc musl-dev perl zlib-dev bzip2-dev xz-dev curl-dev ncurses-dev
+
+  curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VERSION}/minimap2-${MINIMAP2_VERSION}_x64-linux.tar.bz2 | tar -jxf - minimap2-${MINIMAP2_VERSION}_x64-linux/minimap2 \
+    && mv ./minimap2-${MINIMAP2_VERSION}_x64-linux/minimap2 /usr/local/bin
+  curl -L https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 | tar -jxf - \
+    && cd samtools-${SAMTOOLS_VERSION} \
+    && ./configure && make all all-htslib && make install
+  rm -rf samtools-${SAMTOOLS_VERSION}
+
+  apk del curl autoconf automake make gcc musl-dev ncurses-dev