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

DoneSubmitted by 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
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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.scmindex 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
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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.scmindex 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
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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.scmindex 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
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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.scmindex 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
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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.scmindex 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
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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.scmindex 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
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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.scmindex 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
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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.scmindex 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
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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.scmindex 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
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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.scmindex 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
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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.scmindex 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
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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.scmindex 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
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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.scmindex 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
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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.scmindex 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
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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.scmindex 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
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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.scmindex 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
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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
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