reverted back to sortmerna 2.1 from source instead of newer version

their build system is a bit... complex...
MG-RAST · Aug 6, 2019 · a0ffd4f · a0ffd4f
1 parent 4ec9d73
commit a0ffd4f
Showing 1 changed file with 25 additions and 20 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -86,22 +86,23 @@ RUN cd /root \
 	&& sh ./build_simple.sh \
 	&& install -s -m555 diamond /usr/local/bin \
 	&& cd /root \
-	&& rm -rf
+	&& rm -rf *diamond*
 
 ### install latest ea-utils release
 RUN cd /root \
 	&& curl -s https://api.github.com/repos/ExpressionAnalysis/ea-utils/releases/latest  \
 	| grep tarball_url | cut -f4 -d\" | wget -O download.tar.gz -qi - \
 	&& tar xzfp download.tar.gz \
 	&& rm -f download.tar.gz \
-  && cd * \
+  && cd *ea-utils*/clipper \
 	&& make fastq-multx \
 	&& make fastq-join \
 	&& make fastq-mcf \
 	&& install -m755 -s fastq-multx /usr/local/bin \
 	&& install -m755 -s fastq-join /usr/local/bin \
 	&& install -m755 -s fastq-mcf /usr/local/bin \
-	&& cd /root ; rm -rf ea-utils
+	&& cd /root \
+	&& rm -rf *ea-utils*
 
 ### install FragGeneScan from our patched source in github
 RUN cd /root \
@@ -115,7 +116,8 @@ RUN cd /root \
 	&& install -s -m555 FragGeneScan /usr/local/bin/. \
 	&& install -m555 -t /usr/local/bin/. bin/*.pl \
 	&& make clean \
-	&& cd /root ; rm -rf FragGeneScan
+	&& cd /root \
+	&& rm -rf FragGeneScan
 
 
 ### install jellyfish 2.2.6 from source (2.2.8 from repo is broken)
@@ -127,34 +129,35 @@ RUN cd /root \
     && ./configure \
     && make install \
     && cd /root \
-    #&& rm -rf jelly*
+    && rm -rf *jelly*
 
 ### install latest prodigal release
 RUN cd /root \
 		&& curl -s https://api.github.com/repos/hyattpd/Prodigal/releases/latest  \
 		| grep tarball_url | cut -f4 -d\" | wget -O download.tar.gz -qi - \
 		&& tar xzfp download.tar.gz \
 		&& rm -f download.tar.gz \
-		&& cd * \
+		&& cd *Prodigal* \
     && make \
     && make install \
     && strip /usr/local/bin/prodigal \
     && make clean \
-    && cd /root ; rm -rf Prodigal*
-
-### install latest sortmerna 2.1b release
-RUN cd /root \
-	&& curl -s https://api.github.com/repos/biocore/sortmerna/releases/latest  \
-	| grep tarball_url | cut -f4 -d\" | wget -O download.tar.gz -qi - \
-	&& tar xzfp download.tar.gz \
-	&& rm -f download.tar.gz \
-	&& cd * \
+    && cd /root  \
+		&& rm -rf *Prodigal*
+
+	### install sortmerna 2.1b
+	RUN cd /root \
+	&& wget https://github.com/biocore/sortmerna/archive/2.1b.tar.gz \
+	&& tar xvf 2*.tar.gz \
+	&& cd sortmerna-2* \
 	&& sed -i 's/^\#define READLEN [0-9]*/#define READLEN 500000/' include/common.hpp \
 	&& ./configure \
-  && make install \
+	&& make install \
   && make clean \
-  && strip /usr/local/bin/sortmerna* \
-  && cd /root ; rm -rf sortmerna-2*
+  && cd /root \
+	&& rm -rf sortmerna-2* 2*.tar.gz
+
+
 
 ### install skewer
 RUN cd /root \
@@ -163,7 +166,8 @@ RUN cd /root \
     && make \
     && make install \
     && make clean \
-    && cd /root ; rm -rf skewer
+    && cd /root \
+		&& rm -rf skewer
 
 ### install latest vsearch release
 RUN cd /root \
@@ -178,7 +182,8 @@ RUN cd /root \
 		&& make install \
 		&& make clean \
 		&& strip /usr/local/bin/vsearch* \
-		&& cd /root ; rm -rf vsearch-2*
+		&& cd /root \
+		&& rm -rf *vsearch*