20/20: gnu: preseq: Update to 2.0.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit b49c5a58dcbc6f10ebeaef7ccb3d24ff59695db8
Author: Ricardo Wurmus <address@hidden>
Date:   Fri Nov 20 11:14:48 2015 +0100

    gnu: preseq: Update to 2.0.
    
    * gnu/packages/bioinformatics.scm (preseq): Update to 2.0.
    [source]: Add file-name field, remove patches.
    [arguments]: Remove unused build phases, add make flags.
    [inputs]: Add smithlab-cpp.
    * gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: Remove file.
    * gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: Remove
      file.
    * gnu-system.am (dist_patch_DATA): Remove them.
---
 gnu-system.am                                      |    2 -
 gnu/packages/bioinformatics.scm                    |   43 ++++++++-----------
 .../patches/preseq-1.0.2-install-to-PREFIX.patch   |   37 -----------------
 .../patches/preseq-1.0.2-link-with-libbam.patch    |   33 ---------------
 4 files changed, 18 insertions(+), 97 deletions(-)

diff --git a/gnu-system.am b/gnu-system.am
index 32d2286..8a8bf80 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -657,8 +657,6 @@ dist_patch_DATA =                                           
\
   gnu/packages/patches/plotutils-libpng-jmpbuf.patch           \
   gnu/packages/patches/polkit-drop-test.patch                  \
   gnu/packages/patches/portaudio-audacity-compat.patch         \
-  gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch    \
-  gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch     \
   gnu/packages/patches/procps-make-3.82.patch                  \
   gnu/packages/patches/pt-scotch-build-parallelism.patch       \
   gnu/packages/patches/pulseaudio-fix-mult-test.patch          \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4ae1ad0..35cec1e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2590,46 +2590,39 @@ structures, classes for genomic regions, mapped 
sequencing reads, etc.")
 (define-public preseq
   (package
     (name "preseq")
-    (version "1.0.2")
+    (version "2.0")
     (source (origin
               (method url-fetch)
-              (uri
-               (string-append "http://smithlabresearch.org/downloads/preseq-";
-                              version ".tar.bz2"))
+              (uri (string-append "https://github.com/smithlabcode/";
+                                  "preseq/archive/v" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
-               (base32 "0r7sw07p6nv8ygvc17gd78lisbw5336v3vhs86b5wv8mw3pwqksc"))
-              (patches (list (search-patch 
"preseq-1.0.2-install-to-PREFIX.patch")
-                             (search-patch 
"preseq-1.0.2-link-with-libbam.patch")))
+               (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq"))
               (modules '((guix build utils)))
               (snippet
                ;; Remove bundled samtools.
-               '(delete-file-recursively "preseq-master/samtools"))))
+               '(delete-file-recursively "samtools"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ;no "check" target
        #:phases
        (modify-phases %standard-phases
-         (add-after
-          'unpack 'enter-dir
-          (lambda _
-            (chdir "preseq-master")
-            #t))
-         (add-after
-          'enter-dir 'use-samtools-headers
-          (lambda _
-            (substitute* '("smithlab_cpp/SAM.cpp"
-                           "smithlab_cpp/SAM.hpp")
-              (("sam.h") "samtools/sam.h"))
-            #t))
          (delete 'configure))
-       #:make-flags (list (string-append "PREFIX="
-                                         (assoc-ref %outputs "out"))
-                          (string-append "LIBBAM="
-                                         (assoc-ref %build-inputs "samtools")
-                                         "/lib/libbam.a"))))
+       #:make-flags
+       (list (string-append "PREFIX="
+                            (assoc-ref %outputs "out"))
+             (string-append "LIBBAM="
+                            (assoc-ref %build-inputs "samtools")
+                            "/lib/libbam.a")
+             (string-append "SMITHLAB_CPP="
+                            (assoc-ref %build-inputs "smithlab-cpp")
+                            "/lib")
+             "PROGS=preseq"
+             "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp 
$(SAMTOOLS_DIR)")))
     (inputs
      `(("gsl" ,gsl)
        ("samtools" ,samtools-0.1)
+       ("smithlab-cpp" ,smithlab-cpp)
        ("zlib" ,zlib)))
     (home-page "http://smithlabresearch.org/software/preseq/";)
     (synopsis "Program for analyzing library complexity")
diff --git a/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch 
b/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
deleted file mode 100644
index f8318ae..0000000
--- a/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-This patch has been submitted upstream: 
https://github.com/smithlabcode/preseq/pull/15
-
-From 65387b0d766e6c06a15cf8d8f9183d9a4ba644bb Mon Sep 17 00:00:00 2001
-From: Ricardo Wurmus <address@hidden>
-Date: Thu, 25 Jun 2015 15:01:53 +0200
-Subject: [PATCH] Install to PREFIX
-
----
- Makefile | 8 ++++++--
- 1 file changed, 6 insertions(+), 2 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 4d0367a..e334f2f 100644
---- a/preseq-master/Makefile
-+++ b/preseq-master/Makefile
-@@ -22,6 +22,10 @@ ifndef ROOT
- ROOT = $(shell pwd)
- endif
- 
-+ifndef PREFIX
-+PREFIX = $(ROOT)
-+endif
-+
- ifndef SMITHLAB_CPP
- SMITHLAB_CPP=$(ROOT)/smithlab_cpp/
- endif
-@@ -91,8 +95,8 @@ endif
-       $(CXX) $(CXXFLAGS) -o $@ $^ $(INCLUDEARGS) $(LIBS)
- 
- install: $(PROGS)
--      @mkdir -p $(ROOT)/bin
--      @install -m 755 $(PROGS) $(ROOT)/bin
-+      @mkdir -p $(PREFIX)/bin
-+      @install -m 755 $(PROGS) $(PREFIX)/bin
- 
- clean:
-       @-rm -f $(PROGS) *.o *~
diff --git a/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch 
b/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch
deleted file mode 100644
index 035a3b1..0000000
--- a/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-This patch has been submitted upstream: 
https://github.com/smithlabcode/preseq/pull/15
-
-From a937a54d56e8a6ff06237471e568154d1fa5f267 Mon Sep 17 00:00:00 2001
-From: Ricardo Wurmus <address@hidden>
-Date: Thu, 25 Jun 2015 15:02:35 +0200
-Subject: [PATCH] Link with libbam.a if provided via LIBBAM
-
----
- Makefile | 7 +++++++
- 1 file changed, 7 insertions(+)
-
-diff --git a/Makefile b/Makefile
-index e334f2f..de310e4 100644
---- a/preseq-master/Makefile
-+++ b/preseq-master/Makefile
-@@ -83,10 +83,17 @@ $(PROGS): $(addprefix $(SMITHLAB_CPP)/, \
- preseq: continued_fraction.o load_data_for_complexity.o moment_sequence.o
- 
- ifdef SAMTOOLS_DIR
-+ifdef LIBBAM
-+LIBS += -pthread
-+bam2mr preseq: $(addprefix $(SMITHLAB_CPP)/, SAM.o) \
-+        $(LIBBAM)
-+else
- bam2mr preseq: $(addprefix $(SMITHLAB_CPP)/, SAM.o) \
-         $(addprefix $(SAMTOOLS_DIR)/, sam.o bam.o bam_import.o bam_pileup.o \
-         faidx.o bam_aux.o kstring.o knetfile.o sam_header.o razf.o bgzf.o)
- endif
-+endif # SAMTOOLS_DIR
-+
- 
- %.o: %.cpp %.hpp
-       $(CXX) $(CXXFLAGS) -c -o $@ $< $(INCLUDEARGS)