Ticket #42120: cufflinks-2.2.1.diff

science/cufflinks/Portfile

@@ +1 @@
+# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
+
 PortSystem          1.0
+PortGroup           github 1.0
 
-name                cufflinks
-version             0.9.3
+github.setup        cole-trapnell-lab cufflinks 2.2.1 v
 categories          science biology
 platforms           darwin
 maintainers         gmail.com:haroldpimentel
-license             Boost
+license             Boost-1
 
 description         Cufflinks assembles transcripts, estimates their abundances,\
                     and tests for differential expression and regulation in RNA-Seq samples.
@@ -17 +19 @@
                     Cufflinks then estimates the relative abundances of these \
                     transcripts based on how many reads support each one.
 
-homepage            http://cufflinks.cbcb.umd.edu/
-master_sites        ${homepage}downloads
+homepage            http://cole-trapnell-lab.github.io/cufflinks/
+master_sites        ${homepage}assets/downloads/
 
-checksums           sha1        f6c28d8f98569f8d1eae72ff050ce7d2d06bfba4\
-                    rmd160      b9b3b8ec322e79e0e6f2b4b2f23de27b58ec44f4
+checksums           rmd160  6378571ecb06971d1dff5b6ef81a55b36a8be498 \
+                    sha256  e8316b66177914f14b3a0c317e436d386a46c4c212ca1b2326f89f8a2e08d5ae
 
-depends_lib         port:zlib \
+depends_lib         port:boost \
+                    port:eigen3 \
                     port:samtools \
-                    port:boost
+                    port:zlib
+
+configure.args      --with-bam=${prefix} \
+                    --with-boost=${prefix} \
+                    --with-eigen=${prefix} \
+                    --with-zlib=${prefix}
 
-# samtools is not universal
-universal_variant   no
+configure.cppflags-append -isystem${prefix}/include/eigen3
 
 post-destroot {
-    xinstall -d ${destroot}${prefix}/share/doc/${name}
+    xinstall -d ${destroot}${prefix}/share/doc/${subport}
     xinstall -m 644 -W ${worksrcpath} \
         AUTHORS \
         LICENSE \