(address . guix-patches@gnu.org)
87zids20kw.fsf@elephly.net
Here are six bioinfo tools.
--
Ricardo
GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC
Some bioinfo tools
- Done
Details
- 2 participants
- Leo Famulari
- Ricardo Wurmus
- Owner
- unassigned
- Submitted by
- Ricardo Wurmus
- Severity
- normal
R
R
[PATCH 1/6] gnu: Add ritornello.
(address . 27175@debbugs.gnu.org)(name . Ricardo Wurmus)(address . rekado@elephly.net)
20170531211611.14094-1-rekado@elephly.net
* gnu/packages/bioinformatics.scm (ritornello): New variable.
---
gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 45 insertions(+)
Toggle diff (55 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ec69f5020..f2d92a888 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9185,3 +9185,48 @@ working with SAM and BAM files. Current parallelised functionality is
an important subset of samtools functionality, including view, index,
sort, markdup, and depth.")
(license license:gpl2+)))
+
+(define-public ritornello
+ (package
+ (name "ritornello")
+ (version "1.0.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/KlugerLab/"
+ "Ritornello/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "02nik86gq9ljjriv6pamwlmqnfky3ads1fpklx6mc3hx6k40pg38"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; there are no tests
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-samtools-references
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* '("src/SamStream.h"
+ "src/BufferedGenomeReader.h")
+ (("<sam.h>") "<samtools/sam.h>"))
+ #t))
+ (delete 'configure)
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin/")))
+ (mkdir-p bin)
+ (install-file "bin/Ritornello" bin)
+ #t))))))
+ (inputs
+ `(("samtools" ,samtools-0.1)
+ ("fftw" ,fftw)
+ ("boost" ,boost)
+ ("zlib" ,zlib)))
+ (home-page "https://github.com/KlugerLab/Ritornello")
+ (synopsis "Control-free peak caller for ChIP-seq data")
+ (description "Ritornello is a ChIP-seq peak calling algorithm based on
+signal processing that can accurately call binding events without the need to
+do a pair total DNA input or IgG control sample. It has been tested for use
+with narrow binding events such as transcription factor ChIP-seq.")
+ (license license:gpl3+)))
--
2.12.2
R
[PATCH 2/6] gnu: Add trim-galore.
(address . 27175@debbugs.gnu.org)(name . Ricardo Wurmus)(address . rekado@elephly.net)
20170531211611.14094-2-rekado@elephly.net
* gnu/packages/bioinformatics.scm (trim-galore): New variable.
---
gnu/packages/bioinformatics.scm | 60 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 60 insertions(+)
Toggle diff (70 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f2d92a888..d341030b9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9230,3 +9230,63 @@ signal processing that can accurately call binding events without the need to
do a pair total DNA input or IgG control sample. It has been tested for use
with narrow binding events such as transcription factor ChIP-seq.")
(license license:gpl3+)))
+
+(define-public trim-galore
+ (package
+ (name "trim-galore")
+ (version "0.4.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://www.bioinformatics.babraham.ac.uk/"
+ "projects/trim_galore/trim_galore_v"
+ version ".zip"))
+ (sha256
+ (base32
+ "0b9qdxi4521gsrjvbhgky8g7kry9b5nx3byzaxkgxz7p4k8bn1mn"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no tests
+ #:phases
+ (modify-phases %standard-phases
+ ;; The archive contains plain files.
+ (replace 'unpack
+ (lambda* (#:key source #:allow-other-keys)
+ (zero? (system* "unzip" source))))
+ (delete 'configure)
+ (delete 'build)
+ (add-after 'unpack 'hardcode-tool-references
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "trim_galore"
+ (("\\$path_to_cutadapt = 'cutadapt'")
+ (string-append "$path_to_cutadapt = '"
+ (assoc-ref inputs "cutadapt")
+ "/bin/cutadapt'"))
+ (("\\| gzip")
+ (string-append "| "
+ (assoc-ref inputs "gzip")
+ "/bin/gzip"))
+ (("\"gunzip")
+ (string-append "\""
+ (assoc-ref inputs "gzip")
+ "/bin/gunzip")))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out")
+ "/bin")))
+ (mkdir-p bin)
+ (install-file "trim_galore" bin)
+ #t))))))
+ (inputs
+ `(("gzip" ,gzip)
+ ("perl" ,perl)
+ ("cutadapt" ,cutadapt)))
+ (native-inputs
+ `(("unzip" ,unzip)))
+ (home-page "http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/")
+ (synopsis "Wrapper around Cutadapt and FastQC")
+ (description "Trim Galore! is a wrapper script to automate quality and
+adapter trimming as well as quality control, with some added functionality to
+remove biased methylation positions for RRBS sequence files.")
+ (license license:gpl3+)))
--
2.12.2
R
[PATCH 3/6] gnu: Add gess.
(address . 27175@debbugs.gnu.org)(name . Ricardo Wurmus)(address . rekado@elephly.net)
20170531211611.14094-3-rekado@elephly.net
* gnu/packages/bioinformatics.scm (gess): New variable.
---
gnu/packages/bioinformatics.scm | 61 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 61 insertions(+)
Toggle diff (71 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d341030b9..3bab10f8c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9290,3 +9290,64 @@ with narrow binding events such as transcription factor ChIP-seq.")
adapter trimming as well as quality control, with some added functionality to
remove biased methylation positions for RRBS sequence files.")
(license license:gpl3+)))
+
+(define-public gess
+ (package
+ (name "gess")
+ (version "1.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://compbio.uthscsa.edu/"
+ "GESS_Web/files/"
+ "gess-" version ".src.tar.gz"))
+ (sha256
+ (base32
+ "0hyk403kxscclzfs24pvdgiv0wm03kjcziqdrp5w46cb049gz0d7"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no tests
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'build)
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((python (assoc-ref inputs "python"))
+ (out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin/"))
+ (target (string-append
+ out "/lib/python2.7/site-packages/gess/")))
+ (mkdir-p target)
+ (copy-recursively "." target)
+ ;; Make GESS.py executable
+ (chmod (string-append target "GESS.py") #o555)
+ ;; Add Python shebang to the top and make Matplotlib
+ ;; usable.
+ (substitute* (string-append target "GESS.py")
+ (("\"\"\"Description:" line)
+ (string-append "#!" (which "python") "
+import matplotlib
+matplotlib.use('Agg')
+" line)))
+ ;; Make sure GESS has all modules in its path
+ (wrap-program (string-append target "GESS.py")
+ `("PYTHONPATH" ":" prefix (,target ,(getenv "PYTHONPATH"))))
+ (mkdir-p bin)
+ (symlink (string-append target "GESS.py")
+ (string-append bin "GESS.py"))
+ #t))))))
+ (inputs
+ `(("python" ,python-2)
+ ("python2-pysam" ,python2-pysam)
+ ("python2-scipy" ,python2-scipy)
+ ("python2-numpy" ,python2-numpy)
+ ("python2-networkx" ,python2-networkx)
+ ("python2-biopython" ,python2-biopython)))
+ (home-page "http://compbio.uthscsa.edu/GESS_Web/")
+ (synopsis "Detect exon-skipping events from raw RNA-seq data")
+ (description
+ "GESS is an implementation of a novel computational method to detect de
+novo exon-skipping events directly from raw RNA-seq data without the prior
+knowledge of gene annotation information. GESS stands for the graph-based
+exon-skipping scanner detection scheme.")
+ (license license:bsd-3)))
--
2.12.2
R
[PATCH 4/6] gnu: Add phylip.
(address . 27175@debbugs.gnu.org)(name . Ricardo Wurmus)(address . rekado@elephly.net)
20170531211611.14094-4-rekado@elephly.net
* gnu/packages/bioinformatics.scm (phylip): New variable.
---
gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++++++
1 file changed, 37 insertions(+)
Toggle diff (47 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3bab10f8c..55770dea2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9351,3 +9351,40 @@ novo exon-skipping events directly from raw RNA-seq data without the prior
knowledge of gene annotation information. GESS stands for the graph-based
exon-skipping scanner detection scheme.")
(license license:bsd-3)))
+
+(define-public phylip
+ (package
+ (name "phylip")
+ (version "3.696")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://evolution.gs.washington.edu/phylip/"
+ "download/phylip-" version ".tar.gz"))
+ (sha256
+ (base32
+ "01jar1rayhr2gba2pgbw49m56rc5z4p5wn3ds0m188hrlln4a2nd"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no check target
+ #:make-flags (list "-f" "Makefile.unx" "install")
+ #:parallel-build? #f ; not supported
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'enter-dir
+ (lambda _ (chdir "src") #t))
+ (delete 'configure)
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((target (string-append (assoc-ref outputs "out")
+ "/bin")))
+ (mkdir-p target)
+ (for-each (lambda (file)
+ (install-file file target))
+ (find-files "../exe" ".*")))
+ #t)))))
+ (home-page "http://evolution.genetics.washington.edu/phylip/")
+ (synopsis "Tools for inferring phylogenies")
+ (description "PHYLIP (the PHYLogeny Inference Package) is a package of
+programs for inferring phylogenies (evolutionary trees).")
+ (license license:bsd-2)))
--
2.12.2
R
[PATCH 5/6] gnu: Add imp.
(address . 27175@debbugs.gnu.org)(name . Ricardo Wurmus)(address . rekado@elephly.net)
20170531211611.14094-5-rekado@elephly.net
* gnu/packages/bioinformatics.scm (imp): New variable.
---
gnu/packages/bioinformatics.scm | 48 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 48 insertions(+)
Toggle diff (65 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 55770dea2..fa5c32a54 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -85,6 +85,7 @@
#:use-module (gnu packages ruby)
#:use-module (gnu packages serialization)
#:use-module (gnu packages statistics)
+ #:use-module (gnu packages swig)
#:use-module (gnu packages tbb)
#:use-module (gnu packages tex)
#:use-module (gnu packages texinfo)
@@ -9388,3 +9389,50 @@ exon-skipping scanner detection scheme.")
(description "PHYLIP (the PHYLogeny Inference Package) is a package of
programs for inferring phylogenies (evolutionary trees).")
(license license:bsd-2)))
+
+(define-public imp
+ (package
+ (name "imp")
+ (version "2.6.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://integrativemodeling.org/"
+ version "/download/imp-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0lxqx7vh79d771svr611dkilp6sn30qrbw8zvscbrm37v38d2j6h"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(;; FIXME: Some tests fail because they produce warnings, others fail
+ ;; because the PYTHONPATH does not include the modeller's directory.
+ #:tests? #f
+ ;; Do not place libraries in an architecture-specific directory.
+ #:configure-flags
+ (list "-DCMAKE_INSTALL_LIBDIR=lib")))
+ (inputs
+ `(("boost" ,boost)
+ ("gsl" ,gsl)
+ ("swig" ,swig)
+ ("hdf5" ,hdf5)
+ ("fftw" ,fftw)
+ ("python" ,python-2)))
+ (propagated-inputs
+ `(("python2-numpy" ,python2-numpy)
+ ("python2-scipy" ,python2-scipy)
+ ("python2-pandas" ,python2-pandas)
+ ("python2-scikit-learn" ,python2-scikit-learn)
+ ("python2-networkx" ,python2-networkx)))
+ (home-page "https://integrativemodeling.org")
+ (synopsis "Integrative modeling platform")
+ (description "IMP's broad goal is to contribute to a comprehensive
+structural characterization of biomolecules ranging in size and complexity
+from small peptides to large macromolecular assemblies, by integrating data
+from diverse biochemical and biophysical experiments. IMP provides a C++ and
+Python toolbox for solving complex modeling problems, and a number of
+applications for tackling some common problems in a user-friendly way.")
+ ;; IMP is largely available under the GNU Lesser GPL; see the file
+ ;; COPYING.LGPL for the full text of this license. Some IMP modules are
+ ;; available under the GNU GPL (see the file COPYING.GPL).
+ (license (list license:lgpl2.1+
+ license:gpl3+))))
--
2.12.2
R
[PATCH 6/6] gnu: Add tadbit.
(address . 27175@debbugs.gnu.org)(name . Ricardo Wurmus)(address . rekado@elephly.net)
20170531211611.14094-6-rekado@elephly.net
* gnu/packages/bioinformatics.scm (tadbit): New variable.
---
gnu/packages/bioinformatics.scm | 60 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 60 insertions(+)
Toggle diff (70 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fa5c32a54..323a2ee94 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9436,3 +9436,63 @@ applications for tackling some common problems in a user-friendly way.")
;; available under the GNU GPL (see the file COPYING.GPL).
(license (list license:lgpl2.1+
license:gpl3+))))
+
+(define-public tadbit
+ (package
+ (name "tadbit")
+ (version "0.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/3DGenomes/TADbit/"
+ "archive/v" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1cnfqrl4685zar4nnw94j94nhvl2h29jm448nadqi1h05z6fdk4f"))))
+ (build-system python-build-system)
+ (arguments
+ `(;; Tests are included and must be run after installation, but
+ ;; they are incomplete and thus cannot be run.
+ #:tests? #f
+ #:python ,python-2
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fix-problems-with-setup.py
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; setup.py opens these files for writing
+ (chmod "_pytadbit/_version.py" #o664)
+ (chmod "README.rst" #o664)
+
+ ;; Don't attempt to install the bash completions to
+ ;; the home directory.
+ (rename-file "extras/.bash_completion"
+ "extras/tadbit")
+ (substitute* "setup.py"
+ (("\\(path.expanduser\\('~'\\)")
+ (string-append "(\""
+ (assoc-ref outputs "out")
+ "/etc/bash_completion.d\""))
+ (("extras/\\.bash_completion")
+ "extras/tadbit"))
+ #t)))))
+ ;; (native-inputs
+ ;; `(("python2-setuptools" ,python2-setuptools)))
+ (inputs
+ ;; TODO: add Chimera for visualization
+ `(("imp" ,imp)
+ ("mcl" ,mcl)
+ ("python2-scipy" ,python2-scipy)
+ ("python2-numpy" ,python2-numpy)
+ ("python2-matplotlib" ,python2-matplotlib)
+ ("python2-pysam" ,python2-pysam)))
+ (home-page "http://3dgenomes.github.io/TADbit/")
+ (synopsis "Analyze, model, and explore 3C-based data")
+ (description
+ "TADbit is a complete Python library to deal with all steps to analyze,
+model, and explore 3C-based data. With TADbit the user can map FASTQ files to
+obtain raw interaction binned matrices (Hi-C like matrices), normalize and
+correct interaction matrices, identify adn compare the so-called
+@dfn{Topologically Associating Domains} (TADs), build 3D models from the
+interaction matrices, and finally, extract structural properties from the
+models. TADbit is complemented by TADkit for visualizing 3D models.")
+ (license license:gpl3+)))
--
2.12.2
L
(name . Ricardo Wurmus)(address . rekado@elephly.net)(address . 27175@debbugs.gnu.org)
20170602164132.GA27784@jasmine
On Wed, May 31, 2017 at 11:16:11PM +0200, Ricardo Wurmus wrote:
Toggle quote (5 lines)
> * gnu/packages/bioinformatics.scm (tadbit): New variable.
> + ;; (native-inputs
> + ;; `(("python2-setuptools" ,python2-setuptools)))
Do we need this part?
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R
(name . Leo Famulari)(address . leo@famulari.name)(address . 27175-done@debbugs.gnu.org)
87a85idjx6.fsf@elephly.net
Leo Famulari <leo@famulari.name> writes:
Toggle quote (8 lines)
> On Wed, May 31, 2017 at 11:16:11PM +0200, Ricardo Wurmus wrote:
>> * gnu/packages/bioinformatics.scm (tadbit): New variable.
>
>> + ;; (native-inputs
>> + ;; `(("python2-setuptools" ,python2-setuptools)))
>
> Do we need this part?
Oh, no we don’t. Thanks for catching this!
I pushed this series to master with commit 8befd0940.
--
Ricardo
GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC
Closed
?