[PATCH] gnu: Add eXpress.

[PATCH] gnu: Add eXpress.

[Ricardo Wurmus]

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From 16e9535b2dad21cd585b6da94296f94164103de0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 16 Apr 2015 15:16:57 +0200
Subject: [PATCH 1/2] gnu: Add bamtools.

* gnu/packages/bioinformatics.scm (bamtools): New variable.
---
 gnu/packages/bioinformatics.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7da6c75..1e665ba 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -46,6 +46,29 @@
   #:use-module (gnu packages xml)
   #:use-module (gnu packages zip))
 
+(define-public bamtools
+  (package
+    (name "bamtools")
+    (version "2.3.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/pezmaster31/bamtools/archive/v"
+                    version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1brry29bw2xr2l9pqn240rkqwayg85b8qq78zk2zs6nlspk4d018"))))
+    (build-system cmake-build-system)
+    (arguments `(#:tests? #f)) ;no "check" target
+    (inputs `(("zlib" ,zlib)))
+    (home-page "https://github.com/pezmaster31/bamtools")
+    (synopsis "C++ API and command-line toolkit for working with BAM data")
+    (description
+     "BamTools provides both a C++ API and a command-line toolkit for handling
+BAM files.")
+    (license license:expat)))
+
 (define-public bedops
   (package
     (name "bedops")
-- 
2.1.0


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From c65294547718078189bc920be8e5b07d57470060 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 16 Apr 2015 15:18:10 +0200
Subject: [PATCH 2/2] gnu: Add eXpress.

* gnu/packages/bioinformatics.scm (express): New variable.
---
 gnu/packages/bioinformatics.scm | 47 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1e665ba..bb31107 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -28,6 +28,7 @@
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
   #:use-module (gnu packages base)
+  #:use-module (gnu packages boost)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages file)
   #:use-module (gnu packages java)
@@ -37,6 +38,7 @@
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages popt)
+  #:use-module (gnu packages protobuf)
   #:use-module (gnu packages python)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages swig)
@@ -530,6 +532,51 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
 other types of unwanted sequence from high-throughput sequencing reads.")
     (license license:expat)))
 
+(define-public express
+  (package
+    (name "express")
+    (version "1.5.1")
+    (source (origin
+              (method url-fetch)
+              (uri
+               (string-append
+                "http://bio.math.berkeley.edu/eXpress/downloads/express-"
+                version "/express-" version "-src.tgz"))
+              (sha256
+               (base32
+                "03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f ;no "check" target
+       #:phases
+       (alist-cons-after
+        'unpack 'use-shared-boost-libs-and-set-bamtools-paths
+        (lambda* (#:key inputs #:allow-other-keys)
+          (substitute* "CMakeLists.txt"
+            (("set\\(Boost_USE_STATIC_LIBS ON\\)")
+             "set(Boost_USE_STATIC_LIBS OFF)")
+            (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include")
+             (string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
+          (substitute* "src/CMakeLists.txt"
+            (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
+             (string-append (assoc-ref inputs "bamtools") "/lib/bamtools")))
+          #t)
+        %standard-phases)))
+    (inputs
+     `(("boost" ,boost)
+       ("bamtools" ,bamtools)
+       ("protobuf" ,protobuf)
+       ("zlib" ,zlib)))
+    (home-page "http://bio.math.berkeley.edu/eXpress")
+    (synopsis "Streaming quantification for high-throughput genomic sequencing")
+    (description
+     "eXpress is a streaming tool for quantifying the abundances of a set of
+target sequences from sampled subsequences.  Example applications include
+transcript-level RNA-Seq quantification, allele-specific/haplotype expression
+analysis (from RNA-Seq), transcription factor binding quantification in
+ChIP-Seq, and analysis of metagenomic data.")
+    (license license:artistic2.0)))
+
 (define-public fastx-toolkit
   (package
     (name "fastx-toolkit")
-- 
2.1.0

Re: [PATCH] gnu: Add eXpress.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> From 16e9535b2dad21cd585b6da94296f94164103de0 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 16 Apr 2015 15:16:57 +0200
> Subject: [PATCH 1/2] gnu: Add bamtools.
>
> * gnu/packages/bioinformatics.scm (bamtools): New variable.

OK.

> From c65294547718078189bc920be8e5b07d57470060 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 16 Apr 2015 15:18:10 +0200
> Subject: [PATCH 2/2] gnu: Add eXpress.
>
> * gnu/packages/bioinformatics.scm (express): New variable.

[...]

> +       (alist-cons-after
> +        'unpack 'use-shared-boost-libs-and-set-bamtools-paths
> +        (lambda* (#:key inputs #:allow-other-keys)
> +          (substitute* "CMakeLists.txt"
> +            (("set\\(Boost_USE_STATIC_LIBS ON\\)")
> +             "set(Boost_USE_STATIC_LIBS OFF)")

I think the same effect can be achieved by passing
-DBoost_USE_STATIC_LIBS=OFF to cmake (i.e., as #:configure-flags.)
It might be slightly more elegant, but no big deal.

OK!

Ludo’.

Re: [PATCH] gnu: Add eXpress.

[Ricardo Wurmus]

Ludovic Courtès writes:

>> +       (alist-cons-after
>> +        'unpack 'use-shared-boost-libs-and-set-bamtools-paths
>> +        (lambda* (#:key inputs #:allow-other-keys)
>> +          (substitute* "CMakeLists.txt"
>> +            (("set\\(Boost_USE_STATIC_LIBS ON\\)")
>> +             "set(Boost_USE_STATIC_LIBS OFF)")
>
> I think the same effect can be achieved by passing
> -DBoost_USE_STATIC_LIBS=OFF to cmake (i.e., as #:configure-flags.)
> It might be slightly more elegant, but no big deal.

Unfortunately, I haven't been able to get this to work with
#:configure-flags nor with #:make-flags.  I just pushed both commits.q

Thank you for the review!

~~ Ricardo