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

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  • Ricardo Wurmus
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Ricardo Wurmus
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Ricardo Wurmus wrote on 5 Sep 2018 15:46
(address . guix-patches@gnu.org)
idj5zzk2h0t.fsf@bimsb-sys02.mdc-berlin.net
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
R
R
Ricardo Wurmus wrote on 5 Sep 2018 15:54
[PATCH 01/16] gnu: Add python-dill.
(address . 32642@debbugs.gnu.org)(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
20180905135505.10516-1-ricardo.wurmus@mdc-berlin.de
* gnu/packages/python.scm (python-dill): New variable.
---
gnu/packages/python.scm | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)

Toggle diff (37 lines)
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
R
R
Ricardo Wurmus wrote on 5 Sep 2018 15:54
[PATCH 02/16] gnu: Add python-multiprocess.
(address . 32642@debbugs.gnu.org)(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
20180905135505.10516-2-ricardo.wurmus@mdc-berlin.de
* gnu/packages/python.scm (python-multiprocess): New variable.
---
gnu/packages/python.scm | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)

Toggle diff (32 lines)
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
R
R
Ricardo Wurmus wrote on 5 Sep 2018 15:54
[PATCH 03/16] gnu: Add python-toolz.
(address . 32642@debbugs.gnu.org)(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
20180905135505.10516-3-ricardo.wurmus@mdc-berlin.de
* gnu/packages/python.scm (python-toolz): New variable.
---
gnu/packages/python.scm | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)

Toggle diff (32 lines)
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
R
R
Ricardo Wurmus wrote on 5 Sep 2018 15:54
[PATCH 04/16] gnu: Add python-cytoolz.
(address . 32642@debbugs.gnu.org)(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
20180905135505.10516-4-ricardo.wurmus@mdc-berlin.de
* gnu/packages/python.scm (python-cytoolz): New variable.
---
gnu/packages/python.scm | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)

Toggle diff (37 lines)
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
R
R
Ricardo Wurmus wrote on 5 Sep 2018 15:54
[PATCH 05/16] gnu: Add python-sortedcontainers.
(address . 32642@debbugs.gnu.org)(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
20180905135505.10516-5-ricardo.wurmus@mdc-berlin.de
* gnu/packages/python.scm (python-sortedcontainers): New variable.
---
gnu/packages/python.scm | 21 +++++++++++++++++++++
1 file changed, 21 insertions(+)

Toggle diff (31 lines)
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
R
R
Ricardo Wurmus wrote on 5 Sep 2018 15:59
[PATCH 06/16] gnu: Add python-cloudpickle.
(address . 32642@debbugs.gnu.org)(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
20180905140006.10783-1-ricardo.wurmus@mdc-berlin.de
* gnu/packages/python.scm (python-cloudpickle): New variable.
---
gnu/packages/python.scm | 34 ++++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)

Toggle diff (44 lines)
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
R
R
Ricardo Wurmus wrote on 5 Sep 2018 15:59
[PATCH 07/16] gnu: Add python-locket.
(address . 32642@debbugs.gnu.org)(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
20180905140006.10783-2-ricardo.wurmus@mdc-berlin.de
* gnu/packages/python.scm (python-locket): New variable.
---
gnu/packages/python.scm | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)

Toggle diff (29 lines)
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
R
R
Ricardo Wurmus wrote on 5 Sep 2018 15:59
[PATCH 08/16] gnu: Add python-blosc.
(address . 32642@debbugs.gnu.org)(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
20180905140006.10783-3-ricardo.wurmus@mdc-berlin.de
* gnu/packages/python.scm (python-blosc): New variable.
---
gnu/packages/python.scm | 31 +++++++++++++++++++++++++++++++
1 file changed, 31 insertions(+)

Toggle diff (41 lines)
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
R
R
Ricardo Wurmus wrote on 5 Sep 2018 15:59
[PATCH 09/16] gnu: Add python-partd.
(address . 32642@debbugs.gnu.org)(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
20180905140006.10783-4-ricardo.wurmus@mdc-berlin.de
* gnu/packages/python.scm (python-partd): New variable.
---
gnu/packages/python.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)

Toggle diff (35 lines)
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
R
R
Ricardo Wurmus wrote on 5 Sep 2018 16:00
[PATCH 10/16] gnu: Add python-dask.
(address . 32642@debbugs.gnu.org)(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
20180905140006.10783-5-ricardo.wurmus@mdc-berlin.de
* gnu/packages/python.scm (python-dask): New variable.
---
gnu/packages/python.scm | 45 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 45 insertions(+)

Toggle diff (55 lines)
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
R
R
Ricardo Wurmus wrote on 5 Sep 2018 16:00
[PATCH 11/16] gnu: Add python-intervaltree.
(address . 32642@debbugs.gnu.org)(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
20180905140006.10783-6-ricardo.wurmus@mdc-berlin.de
* gnu/packages/bioinformatics.scm (python-intervaltree): New variable.
---
gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++
1 file changed, 28 insertions(+)

Toggle diff (38 lines)
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
R
R
Ricardo Wurmus wrote on 5 Sep 2018 16:00
[PATCH 12/16] gnu: Add python-pypairix.
(address . 32642@debbugs.gnu.org)(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
20180905140006.10783-7-ricardo.wurmus@mdc-berlin.de
* gnu/packages/bioinformatics.scm (python-pypairix): New variable.
---
gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)

Toggle diff (34 lines)
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
R
R
Ricardo Wurmus wrote on 5 Sep 2018 16:00
[PATCH 13/16] gnu: Add python-pyfaidx.
(address . 32642@debbugs.gnu.org)(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
20180905140006.10783-8-ricardo.wurmus@mdc-berlin.de
* gnu/packages/bioinformatics.scm (python-pyfaidx): New variable.
---
gnu/packages/bioinformatics.scm | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)

Toggle diff (32 lines)
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
R
R
Ricardo Wurmus wrote on 5 Sep 2018 16:00
[PATCH 14/16] gnu: Add python-cooler.
(address . 32642@debbugs.gnu.org)(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
20180905140006.10783-9-ricardo.wurmus@mdc-berlin.de
* gnu/packages/bioinformatics.scm (python-cooler): 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 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
R
R
Ricardo Wurmus wrote on 5 Sep 2018 16:07
[PATCH 15/16] gnu: Add python-hicexplorer.
(address . 32642@debbugs.gnu.org)(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
20180905140728.11138-1-ricardo.wurmus@mdc-berlin.de
* gnu/packages/bioinformatics.scm (python-hicexplorer): New variable.
---
gnu/packages/bioinformatics.scm | 53 +++++++++++++++++++++++++++++++++
1 file changed, 53 insertions(+)

Toggle diff (63 lines)
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
R
R
Ricardo Wurmus wrote on 5 Sep 2018 16:07
[PATCH 16/16] gnu: Add python-pygenometracks.
(address . 32642@debbugs.gnu.org)(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
20180905140728.11138-2-ricardo.wurmus@mdc-berlin.de
* gnu/packages/bioinformatics.scm (python-pygenometracks): New variable.
---
gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++
1 file changed, 31 insertions(+)

Toggle diff (41 lines)
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
R
R
Ricardo Wurmus wrote on 10 Sep 2018 16:52
(address . 32642-done@debbugs.gnu.org)
87k1ntl804.fsf@mdc-berlin.de
Toggle quote (3 lines)
> * gnu/packages/bioinformatics.scm (python-pygenometracks): New variable.
> ---

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

--
Ricardo
Closed
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