[bug#32642] [PATCH 00/16] gnu: Add python-pygenometracks.

[bug#32642] [PATCH 00/16] gnu: Add python-pygenometracks.

[Ricardo Wurmus]

Hi Guix,

this patch set adds pygenometracks and dependencies.

Ricardo Wurmus (16):
  gnu: Add python-dill.
  gnu: Add python-multiprocess.
  gnu: Add python-toolz.
  gnu: Add python-cytoolz.
  gnu: Add python-sortedcontainers.
  gnu: Add python-cloudpickle.
  gnu: Add python-locket.
  gnu: Add python-blosc.
  gnu: Add python-partd.
  gnu: Add python-dask.
  gnu: Add python-intervaltree.
  gnu: Add python-pypairix.
  gnu: Add python-pyfaidx.
  gnu: Add python-cooler.
  gnu: Add python-hicexplorer.
  gnu: Add python-pygenometracks.

 gnu/packages/bioinformatics.scm | 195 +++++++++++++++++++++++
 gnu/packages/python.scm         | 273 ++++++++++++++++++++++++++++++++
 2 files changed, 468 insertions(+)

-- 
2.18.0

[bug#32642] [PATCH 01/16] gnu: Add python-dill.

[Ricardo Wurmus]

* gnu/packages/python.scm (python-dill): New variable.
---
 gnu/packages/python.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 8c7c9d3c3..b547592a2 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -14018,3 +14018,30 @@ scalable way of keeping track of data together with learned annotations and
 reduces the code overhead typically encountered when using a mostly
 object-oriented library such as @code{scikit-learn}.")
     (license license:bsd-3)))
+
+(define-public python-dill
+  (package
+    (name "python-dill")
+    (version "0.2.8.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "dill" version))
+       (sha256
+        (base32
+         "1cymzn9fxwdy33h21zkk4gqgzvd25110hh3zdqnvnwa3p52c4kb2"))))
+    (build-system python-build-system)
+    ;; FIXME: The check phase fails with "don't know how to make test".
+    (arguments '(#:tests? #f))
+    (home-page "https://pypi.org/project/dill")
+    (synopsis "Serialize all of Python")
+    (description "Dill extends Python's @code{pickle} module for serializing
+and de-serializing Python objects to the majority of the built-in Python
+types.  Dill provides the user the same interface as the @code{pickle} module,
+and also includes some additional features.  In addition to pickling Python
+objects, @code{dill} provides the ability to save the state of an interpreter
+session in a single command.  Hence, it would be feasable to save a
+interpreter session, close the interpreter, ship the pickled file to another
+computer, open a new interpreter, unpickle the session and thus continue from
+the saved state of the original interpreter session.")
+    (license license:bsd-3)))
-- 
2.18.0

[bug#32642] [PATCH 02/16] gnu: Add python-multiprocess.

[Ricardo Wurmus]

* gnu/packages/python.scm (python-multiprocess): New variable.
---
 gnu/packages/python.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index b547592a2..9da7072aa 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -14045,3 +14045,25 @@ interpreter session, close the interpreter, ship the pickled file to another
 computer, open a new interpreter, unpickle the session and thus continue from
 the saved state of the original interpreter session.")
     (license license:bsd-3)))
+
+(define-public python-multiprocess
+  (package
+    (name "python-multiprocess")
+    (version "0.70.6.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "multiprocess" version))
+       (sha256
+        (base32
+         "1ip5caz67b3q0553mr8gm8xwsb8x500jn8ml0gihgyfy52m2ypcq"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-dill" ,python-dill)))
+    (home-page "https://pypi.org/project/multiprocess")
+    (synopsis "Multiprocessing and multithreading in Python")
+    (description
+     "This package is a fork of the multiprocessing Python package, a package
+which supports the spawning of processes using the API of the standard
+library's @code{threading} module.")
+    (license license:bsd-3)))
-- 
2.18.0

[bug#32642] [PATCH 03/16] gnu: Add python-toolz.

[Ricardo Wurmus]

* gnu/packages/python.scm (python-toolz): New variable.
---
 gnu/packages/python.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 9da7072aa..80c36671a 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -14067,3 +14067,25 @@ the saved state of the original interpreter session.")
 which supports the spawning of processes using the API of the standard
 library's @code{threading} module.")
     (license license:bsd-3)))
+
+(define-public python-toolz
+  (package
+    (name "python-toolz")
+    (version "0.9.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "toolz" version))
+       (sha256
+        (base32
+         "1j9i7fdjnx9dz35fdj5gvgxx6585ja9sxgaiv65if77nlxz0m7wj"))))
+    (build-system python-build-system)
+    ;; FIXME: tests cannot be computed: "Can't perform this operation for
+    ;; unregistered loader type"
+    (arguments '(#:tests? #f))
+    (home-page "https://github.com/pytoolz/toolz/")
+    (synopsis "List processing tools and functional utilities")
+    (description
+     "This package provides a set of utility functions for iterators,
+functions, and dictionaries.")
+    (license license:bsd-3)))
-- 
2.18.0

[bug#32642] [PATCH 04/16] gnu: Add python-cytoolz.

[Ricardo Wurmus]

* gnu/packages/python.scm (python-cytoolz): New variable.
---
 gnu/packages/python.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 80c36671a..3ee894098 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -14089,3 +14089,30 @@ library's @code{threading} module.")
      "This package provides a set of utility functions for iterators,
 functions, and dictionaries.")
     (license license:bsd-3)))
+
+(define-public python-cytoolz
+  (package
+    (name "python-cytoolz")
+    (version "0.9.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "cytoolz" version))
+       (sha256
+        (base32
+         "1r80p88hm3f3r4zpixzr047y5hw4bzy41m4xywnhycda83x0dk44"))))
+    (build-system python-build-system)
+    ;; FIXME: tests fail with "module 'cytoolz.curried' has no attribute
+    ;; 'exceptions'"
+    (arguments '(#:tests? #f))
+    (propagated-inputs
+     `(("python-toolz" ,python-toolz)))
+    (native-inputs
+     `(("python-cython" ,python-cython)))
+    (home-page "https://github.com/pytoolz/cytoolz")
+    (synopsis "High performance functional utilities")
+    (description
+     "The cytoolz package implements the same API as provided by toolz.  The
+main differences are that @code{cytoolz} is faster and cytoolz offers a C API
+that is accessible to other projects developed in Cython.")
+    (license license:bsd-3)))
-- 
2.18.0

[bug#32642] [PATCH 05/16] gnu: Add python-sortedcontainers.

[Ricardo Wurmus]

* gnu/packages/python.scm (python-sortedcontainers): New variable.
---
 gnu/packages/python.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 3ee894098..0eceefdc6 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -14116,3 +14116,24 @@ functions, and dictionaries.")
 main differences are that @code{cytoolz} is faster and cytoolz offers a C API
 that is accessible to other projects developed in Cython.")
     (license license:bsd-3)))
+
+(define-public python-sortedcontainers
+  (package
+    (name "python-sortedcontainers")
+    (version "2.0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "sortedcontainers" version))
+       (sha256
+        (base32
+         "10hrk2k0hbf9x78vd3f0lj277m1yzfhzzxr0hja718liwb398wk0"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-tox" ,python-tox)))
+    (home-page "http://www.grantjenks.com/docs/sortedcontainers/")
+    (synopsis "Sorted List, Sorted Dict, Sorted Set")
+    (description
+     "This package provides a sorted collections library, written in
+pure-Python.")
+    (license license:asl2.0)))
-- 
2.18.0

[bug#32642] [PATCH 06/16] gnu: Add python-cloudpickle.

[Ricardo Wurmus]

* gnu/packages/python.scm (python-cloudpickle): New variable.
---
 gnu/packages/python.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 0eceefdc6..501387c02 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -14137,3 +14137,37 @@ that is accessible to other projects developed in Cython.")
      "This package provides a sorted collections library, written in
 pure-Python.")
     (license license:asl2.0)))
+
+(define-public python-cloudpickle
+  (package
+    (name "python-cloudpickle")
+    (version "0.5.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "cloudpickle" version))
+       (sha256
+        (base32
+         "0gdg5n025v4wqmdg65rm0n6fvp6731ip30ji0rmn2kqsyr4bb93f"))))
+    (build-system python-build-system)
+    ;; FIXME: there are 5 errors in 122 tests:
+    ;; ERROR: test_function_pickle_compat_0_4_0 (tests.cloudpickle_test.CloudPickleTest)
+    ;; ERROR: test_function_pickle_compat_0_4_1 (tests.cloudpickle_test.CloudPickleTest)
+    ;; ERROR: test_function_pickle_compat_0_4_0 (tests.cloudpickle_test.Protocol2CloudPickleTest)
+    ;; ERROR: test_function_pickle_compat_0_4_1 (tests.cloudpickle_test.Protocol2CloudPickleTest)
+    ;; ERROR: test_temp_file (tests.cloudpickle_file_test.CloudPickleFileTests)
+    ;; TypeError: cannot serialize '_io.BufferedRandom' object
+    (arguments '(#:tests? #f))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-mock" ,python-mock)
+       ("python-tornado" ,python-tornado)))
+    (home-page "https://github.com/cloudpipe/cloudpickle")
+    (synopsis "Extended pickling support for Python objects")
+    (description
+     "Cloudpickle makes it possible to serialize Python constructs not
+supported by the default pickle module from the Python standard library.  It
+is especially useful for cluster computing where Python expressions are
+shipped over the network to execute on remote hosts, possibly close to the
+data.")
+    (license license:bsd-3)))
-- 
2.18.0

[bug#32642] [PATCH 07/16] gnu: Add python-locket.

[Ricardo Wurmus]

* gnu/packages/python.scm (python-locket): New variable.
---
 gnu/packages/python.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 501387c02..2ac5c9f44 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -14171,3 +14171,22 @@ is especially useful for cluster computing where Python expressions are
 shipped over the network to execute on remote hosts, possibly close to the
 data.")
     (license license:bsd-3)))
+
+(define-public python-locket
+  (package
+    (name "python-locket")
+    (version "0.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "locket" version))
+       (sha256
+        (base32
+         "1d4z2zngrpqkrfhnd4yhysh66kjn4mblys2l06sh5dix2p0n7vhz"))))
+    (build-system python-build-system)
+    (home-page "https://github.com/mwilliamson/locket.py")
+    (synopsis "File-based locks for Python")
+    (description
+     "Locket implements a lock that can be used by multiple processes provided
+they use the same path.")
+    (license license:bsd-2)))
-- 
2.18.0

[bug#32642] [PATCH 08/16] gnu: Add python-blosc.

[Ricardo Wurmus]

* gnu/packages/python.scm (python-blosc): New variable.
---
 gnu/packages/python.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 2ac5c9f44..f0e228483 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -14190,3 +14190,34 @@ data.")
      "Locket implements a lock that can be used by multiple processes provided
 they use the same path.")
     (license license:bsd-2)))
+
+(define-public python-blosc
+  (package
+    (name "python-blosc")
+    (version "1.5.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "blosc" version))
+       (sha256
+        (base32
+         "1cm91c6r431yla2mbs4895bgiianjf30dfz14vvv99dslygd65jw"))))
+    (build-system python-build-system)
+    ;; FIXME: all tests pass, but then this error is printed:
+    ;; TypeError: calling <function run at 0x7ffff2568d90> returned None, not a test
+    (arguments '(#:tests? #f))
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)))
+    (home-page "https://github.com/blosc/python-blosc")
+    (synopsis "Python wrapper for the Blosc data compressor library")
+    (description "Blosc is a high performance compressor optimized for binary
+data.  It has been designed to transmit data to the processor cache faster
+than the traditional, non-compressed, direct memory fetch approach via a
+@code{memcpy()} system call.
+
+Blosc works well for compressing numerical arrays that contains data with
+relatively low entropy, like sparse data, time series, grids with
+regular-spaced values, etc.
+
+This Python package wraps the Blosc library.")
+    (license license:bsd-3)))
-- 
2.18.0

[bug#32642] [PATCH 09/16] gnu: Add python-partd.

[Ricardo Wurmus]

* gnu/packages/python.scm (python-partd): New variable.
---
 gnu/packages/python.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index f0e228483..8429ad32f 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -14221,3 +14221,28 @@ regular-spaced values, etc.
 
 This Python package wraps the Blosc library.")
     (license license:bsd-3)))
+
+(define-public python-partd
+  (package
+    (name "python-partd")
+    (version "0.3.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "partd" version))
+       (sha256
+        (base32
+         "03s0i5qfgkx6y24bmfgyd5hnsjznkbbfafwb2khf7k9790f1yab7"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-blosc" ,python-blosc)
+       ("python-locket" ,python-locket)
+       ("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
+       ("python-pyzmq" ,python-pyzmq)
+       ("python-toolz" ,python-toolz)))
+    (home-page "https://github.com/dask/partd/")
+    (synopsis "Appendable key-value storage")
+    (description "Partd stores key-value pairs.  Values are raw bytes.  We
+append on old values.  Partd excels at shuffling operations.")
+    (license license:bsd-3)))
-- 
2.18.0

[bug#32642] [PATCH 10/16] gnu: Add python-dask.

[Ricardo Wurmus]

* gnu/packages/python.scm (python-dask): New variable.
---
 gnu/packages/python.scm | 45 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 8429ad32f..6e06125d9 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -14246,3 +14246,48 @@ This Python package wraps the Blosc library.")
     (description "Partd stores key-value pairs.  Values are raw bytes.  We
 append on old values.  Partd excels at shuffling operations.")
     (license license:bsd-3)))
+
+(define-public python-dask
+  (package
+    (name "python-dask")
+    (version "0.19.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "dask" version))
+       (sha256
+        (base32
+         "1pm1163qb6s22p8fnvj0zlfazihvs7hxjn8l2n52bzs7shw6kdz3"))))
+    (build-system python-build-system)
+    ;; A single test out of 5000+ fails.  This test is marked as xfail when
+    ;; pytest-xdist is used.
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'disable-broken-test
+           (lambda _
+             (substitute* "dask/tests/test_threaded.py"
+               (("def test_interrupt\\(\\)" m)
+                (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
+                               m)))
+             #t)))))
+    (propagated-inputs
+     `(("python-cloudpickle" ,python-cloudpickle)
+       ("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
+       ("python-partd" ,python-partd)
+       ("python-toolz" ,python-toolz)
+       ("python-pyyaml" ,python-pyyaml)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-pytest-runner" ,python-pytest-runner)))
+    (home-page "https://github.com/dask/dask/")
+    (synopsis "Parallel computing with task scheduling")
+    (description
+     "Dask is a flexible parallel computing library for analytics.  It
+consists of two components: dynamic task scheduling optimized for computation,
+and large data collections like parallel arrays, dataframes, and lists that
+extend common interfaces like NumPy, Pandas, or Python iterators to
+larger-than-memory or distributed environments.  These parallel collections
+run on top of the dynamic task schedulers. ")
+    (license license:bsd-3)))
-- 
2.18.0

[bug#32642] [PATCH 11/16] gnu: Add python-intervaltree.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (python-intervaltree): New variable.
---
 gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 05d516165..963715b43 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13551,3 +13551,31 @@ reference transcripts provided in a annotation file (also in GTF/GFF3 format).
        (list
         license:expat                   ;license for gffcompare
         license:artistic2.0)))))        ;license for gclib
+
+(define-public python-intervaltree
+  (package
+    (name "python-intervaltree")
+    (version "2.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "intervaltree" version))
+       (sha256
+        (base32
+         "02w191m9zxkcjqr1kv2slxvhymwhj3jnsyy3a28b837pi15q19dc"))))
+    (build-system python-build-system)
+    ;; FIXME: error when collecting tests
+    (arguments '(#:tests? #f))
+    (propagated-inputs
+     `(("python-sortedcontainers" ,python-sortedcontainers)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
+    (home-page "https://github.com/chaimleib/intervaltree")
+    (synopsis "Editable interval tree data structure")
+    (description
+     "This package provides a mutable, self-balancing interval tree
+implementation for Python.  Queries may be by point, by range overlap, or by
+range envelopment.  This library was designed to allow tagging text and time
+intervals, where the intervals include the lower bound but not the upper
+bound.")
+    (license license:asl2.0)))
-- 
2.18.0

[bug#32642] [PATCH 12/16] gnu: Add python-pypairix.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (python-pypairix): New variable.
---
 gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 963715b43..466e40242 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13579,3 +13579,27 @@ range envelopment.  This library was designed to allow tagging text and time
 intervals, where the intervals include the lower bound but not the upper
 bound.")
     (license license:asl2.0)))
+
+(define-public python-pypairix
+  (package
+    (name "python-pypairix")
+    (version "0.3.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pypairix" version))
+       (sha256
+        (base32
+         "0zs92b74s5v4xy2h16s15f3z6l4nnbw8x8zyif7xx5xpafjn0xss"))))
+    (build-system python-build-system)
+    ;; FIXME: the tests fail because test.support cannot be loaded:
+    ;; ImportError: cannot import name 'support'
+    (arguments '(#:tests? #f))
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "https://github.com/4dn-dcic/pairix")
+    (synopsis "Support for querying pairix-indexed bgzipped text files")
+    (description
+     "Pypairix is a Python module for fast querying on a pairix-indexed
+bgzipped text file that contains a pair of genomic coordinates per line.")
+    (license license:expat)))
-- 
2.18.0

[bug#32642] [PATCH 13/16] gnu: Add python-pyfaidx.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (python-pyfaidx): New variable.
---
 gnu/packages/bioinformatics.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 466e40242..624bae95d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13603,3 +13603,25 @@ bound.")
      "Pypairix is a Python module for fast querying on a pairix-indexed
 bgzipped text file that contains a pair of genomic coordinates per line.")
     (license license:expat)))
+
+(define-public python-pyfaidx
+  (package
+    (name "python-pyfaidx")
+    (version "0.5.4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pyfaidx" version))
+       (sha256
+        (base32
+         "0y5zyjksj1rdglj601xd2bbni5abhdh622y3ck76chyzxz9z4rx8"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-setuptools" ,python-setuptools)
+       ("python-six" ,python-six)))
+    (home-page "http://mattshirley.com")
+    (synopsis "Random access to fasta subsequences")
+    (description
+     "This package provides procedures for efficient pythonic random access to
+fasta subsequences.")
+    (license license:bsd-3)))
-- 
2.18.0

[bug#32642] [PATCH 14/16] gnu: Add python-cooler.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (python-cooler): New variable.
---
 gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 624bae95d..e555fb009 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13625,3 +13625,40 @@ bgzipped text file that contains a pair of genomic coordinates per line.")
      "This package provides procedures for efficient pythonic random access to
 fasta subsequences.")
     (license license:bsd-3)))
+
+(define-public python-cooler
+  (package
+    (name "python-cooler")
+    (version "0.7.11")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "cooler" version))
+       (sha256
+        (base32
+         "08k5nxnxa6qsbk15z5z0q01n28042k87wi4905hh95rzqib15mhx"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-biopython" ,python-biopython)
+       ("python-click" ,python-click)
+       ("python-cytoolz" ,python-cytoolz)
+       ("python-dask" ,python-dask)
+       ("python-h5py" ,python-h5py)
+       ("python-multiprocess" ,python-multiprocess)
+       ("python-pandas" ,python-pandas)
+       ("python-pyfaidx" ,python-pyfaidx)
+       ("python-pypairix" ,python-pypairix)
+       ("python-pysam" ,python-pysam)
+       ("python-scipy" ,python-scipy)))
+    (native-inputs
+     `(("python-mock" ,python-mock)
+       ("python-nose" ,python-nose)
+       ("python-numpydoc" ,python-numpydoc)
+       ("python-sphinx" ,python-sphinx)))
+    (home-page "https://github.com/mirnylab/cooler")
+    (synopsis "Sparse binary format for genomic interaction matrices")
+    (description
+     "Cooler is a support library for a sparse, compressed, binary persistent
+storage format, called @code{cool}, used to store genomic interaction data,
+such as Hi-C contact matrices.")
+    (license license:bsd-3)))
-- 
2.18.0

[bug#32642] [PATCH 15/16] gnu: Add python-hicexplorer.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (python-hicexplorer): New variable.
---
 gnu/packages/bioinformatics.scm | 53 +++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e555fb009..ccc3ed26a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13662,3 +13662,56 @@ fasta subsequences.")
 storage format, called @code{cool}, used to store genomic interaction data,
 such as Hi-C contact matrices.")
     (license license:bsd-3)))
+
+(define-public python-hicexplorer
+  (package
+    (name "python-hicexplorer")
+    (version "2.1.4")
+    (source
+     (origin
+       ;; The latest version is not available on Pypi.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/deeptools/HiCExplorer.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0q5gpbzmrkvygqgw524q36b4nrivcmyi5v194vsx0qw7b3gcmq08"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'loosen-up-requirements
+           (lambda _
+             (substitute* "setup.py"
+               (("==") ">="))
+             #t)))))
+    (propagated-inputs
+     `(("python-biopython" ,python-biopython)
+       ("python-configparser" ,python-configparser)
+       ("python-cooler" ,python-cooler)
+       ("python-future" ,python-future)
+       ("python-intervaltree" ,python-intervaltree)
+       ("python-jinja2" ,python-jinja2)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
+       ("python-pybigwig" ,python-pybigwig)
+       ("python-pysam" ,python-pysam)
+       ("python-scipy" ,python-scipy)
+       ("python-six" ,python-six)
+       ("python-tables" ,python-tables)
+       ("python-unidecode" ,python-unidecode)))
+    (home-page "http://hicexplorer.readthedocs.io")
+    (synopsis "Process, analyze and visualize Hi-C data")
+    (description
+     "HiCExplorer is a powerful and easy to use set of tools to process,
+normalize and visualize Hi-C data.  HiCExplorer facilitates the creation of
+contact matrices, correction of contacts, TAD detection, A/B compartments,
+merging, reordering or chromosomes, conversion from different formats
+including cooler and detection of long-range contacts.  Moreover, it allows
+the visualization of multiple contact matrices along with other types of data
+like genes, compartments, ChIP-seq coverage tracks (and in general any type of
+genomic scores), long range contacts and the visualization of viewpoints.")
+    (license license:gpl3)))
-- 
2.18.0

[bug#32642] [PATCH 16/16] gnu: Add python-pygenometracks.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (python-pygenometracks): New variable.
---
 gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ccc3ed26a..97e8e1b07 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13715,3 +13715,34 @@ the visualization of multiple contact matrices along with other types of data
 like genes, compartments, ChIP-seq coverage tracks (and in general any type of
 genomic scores), long range contacts and the visualization of viewpoints.")
     (license license:gpl3)))
+
+(define-public python-pygenometracks
+  (package
+    (name "python-pygenometracks")
+    (version "2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pyGenomeTracks" version))
+       (sha256
+        (base32
+         "1fws6bqsyy9kj3qiabhkqx4wd4i775gsxnhszqd3zg7w67sc1ic5"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-configparser" ,python-configparser)
+       ("python-future" ,python-future)
+       ("python-hicexplorer" ,python-hicexplorer)
+       ("python-intervaltree" ,python-intervaltree)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-numpy" ,python-numpy)
+       ("python-pybigwig" ,python-pybigwig)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
+    (home-page "https://pygenometracks.readthedocs.io")
+    (synopsis "Program and library to plot beautiful genome browser tracks")
+    (description
+     "This package aims to produce high-quality genome browser tracks that
+are highly customizable.  Currently, it is possible to plot: bigwig, bed (many
+options), bedgraph, links (represented as arcs), and Hi-C matrices.
+pyGenomeTracks can make plots with or without Hi-C data.")
+    (license license:gpl3+)))
-- 
2.18.0

bug#32642: [PATCH 16/16] gnu: Add python-pygenometracks.

[Ricardo Wurmus]

> * gnu/packages/bioinformatics.scm (python-pygenometracks): New variable.
> ---

Pushed this series of patches to “master” with commit 5bfa7510d.

--
Ricardo