From a79ad5fce57c271f22441df8a21c04d95fc772d5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Aug 2021 15:23:20 +0200
Subject: gnu: pigx-rnaseq: Update to 0.0.19.

* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.19.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4ac9a99b41..5785e27a85 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10447,7 +10447,7 @@ (define-public dropseq-tools
 (define-public pigx-rnaseq
   (package
     (name "pigx-rnaseq")
-    (version "0.0.18")
+    (version "0.0.19")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
@@ -10455,7 +10455,7 @@ (define-public pigx-rnaseq
                                   "/pigx_rnaseq-" version ".tar.gz"))
               (sha256
                (base32
-                "1622l6grmsk0wm859rvllngx29q3v16jjvzcdq2bmrlamccrj82y"))))
+                "1ja3bda1appxrzbfy7wp7khy30mm7lic8xbq3gkbpc5bld3as9cm"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-tests? #f             ; not supported
-- 
cgit v1.2.3


From 27952318a58fe264080c351615cc73d40ed458c0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 20 Aug 2021 10:42:11 +0200
Subject: gnu: fastp: Update to 0.20.1.

* gnu/packages/bioinformatics.scm (fastp): Update to 0.20.1.
[arguments]: Set PREFIX instead of BINDIR.
---
 gnu/packages/bioinformatics.scm | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5785e27a85..426926a37c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4583,7 +4583,7 @@ (define-public fastqc
 (define-public fastp
   (package
     (name "fastp")
-    (version "0.14.1")
+    (version "0.20.1")
     (source
      (origin
        (method git-fetch)
@@ -4593,19 +4593,18 @@ (define-public fastp
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1r6ms5zbf5rps4rgp4z73nczadl00b5rqylw8f684isfz27dp0xh"))))
+         "0ly8mxdvrcy23jwxyppysx3dhb1lwsqhfbgpyvargxhfk6k700x4"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; there are none
        #:make-flags
-       (list (string-append "BINDIR=" (assoc-ref %outputs "out") "/bin"))
+       (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)
          (add-before 'install 'create-target-dir
            (lambda* (#:key outputs #:allow-other-keys)
-             (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
-             #t)))))
+             (mkdir-p (string-append (assoc-ref outputs "out") "/bin")))))))
     (inputs
      `(("zlib" ,zlib)))
     (home-page "https://github.com/OpenGene/fastp/")
-- 
cgit v1.2.3


From f66759e0b2410aaa2ad8e74ef5c0aaf728abb6ba Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 25 Aug 2021 11:21:42 +0200
Subject: gnu: Add ivar.

* gnu/packages/bioinformatics.scm (ivar): New variable.
---
 gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 426926a37c..e663ff2591 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14272,6 +14272,32 @@ (define-public lofreq
 usually ignored by other methods or only used for filtering.")
     (license license:expat)))
 
+(define-public ivar
+  (package
+    (name "ivar")
+    (version "1.3.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/andersen-lab/ivar")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "044xa0hm3b8fga64csrdx05ih8w7kwmvcdrdrhkg8j11ml4bi4xv"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("htslib" ,htslib)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)))
+    (home-page "https://andersen-lab.github.io/ivar/html/")
+    (synopsis "Tools for amplicon-based sequencing")
+    (description "iVar is a computational package that contains functions
+broadly useful for viral amplicon-based sequencing. ")
+    (license license:gpl3+)))
+
 (define-public python-pyliftover
   (package
     (name "python-pyliftover")
-- 
cgit v1.2.3


From 17c765e2e1b425c5be06bb1701749656e3d84f4b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 27 Aug 2021 13:24:19 +0200
Subject: gnu: Add r-cytonorm.

* gnu/packages/bioinformatics.scm (r-cytonorm): New variable.
---
 gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e663ff2591..1775f5a15e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14903,3 +14903,42 @@ (define-public r-spectre
 integration, exploration, and analysis of high-dimensional single-cell
 cytometry and imaging data.")
       (license license:expat))))
+
+(define-public r-cytonorm
+  (let ((commit "e4b9d343ee65db3c422800f1db3e77c25abde987")
+        (revision "1"))
+    (package
+      (name "r-cytonorm")
+      (version (git-version "0.0.7" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/saeyslab/CytoNorm")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "0h2rdy15i4zymd4dv60n5w0frbsdbmzpv99dgm0l2dn041qv7fah"))))
+      (properties `((upstream-name . "CytoNorm")))
+      (build-system r-build-system)
+      (propagated-inputs
+       `(("r-cytoml" ,r-cytoml)
+         ("r-dplyr" ,r-dplyr)
+         ("r-emdist" ,r-emdist)
+         ("r-flowcore" ,r-flowcore)
+         ("r-flowsom" ,r-flowsom)
+         ("r-flowworkspace" ,r-flowworkspace)
+         ("r-ggplot2" ,r-ggplot2)
+         ("r-gridextra" ,r-gridextra)
+         ("r-pheatmap" ,r-pheatmap)
+         ("r-stringr" ,r-stringr)))
+      (home-page "https://github.com/saeyslab/CytoNorm")
+      (synopsis "Normalize cytometry data measured across multiple batches")
+      (description
+       "This package can be used to normalize cytometry samples when a control
+sample is taken along in each of the batches.  This is done by first
+identifying multiple clusters/cell types, learning the batch effects from the
+control samples and applying quantile normalization on all markers of
+interest.")
+      (license license:gpl2+))))
-- 
cgit v1.2.3


From db13eb962f5822647cbc88321031615a39d1ff15 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 27 Aug 2021 13:24:33 +0200
Subject: gnu: Add python-strawc.

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

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1775f5a15e..0979a86d8d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14773,6 +14773,28 @@ (define-public nanosv
 instruments, or Pacific Biosciences RSII or Sequel sequencers.")
    (license license:expat)))
 
+(define-public python-strawc
+  (package
+    (name "python-strawc")
+    (version "0.0.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "strawC" version))
+       (sha256
+        (base32
+         "1z1gy8n56lhriy6hdkh9r82ndikndipq2cy2wh8q185qig4rimr6"))))
+    (build-system python-build-system)
+    (inputs
+     `(("curl" ,curl)
+       ("pybind11" ,pybind11)
+       ("zlib" ,zlib)))
+    (home-page "https://github.com/aidenlab/straw")
+    (synopsis "Stream data from .hic files")
+    (description "Straw is library which allows rapid streaming of contact
+data from @file{.hic} files.  This package provides Python bindings.")
+    (license license:expat)))
+
 (define-public r-ascat
   (package
    (name "r-ascat")
-- 
cgit v1.2.3


From e85b35070caa41926b52625ef0fa828d6acc8271 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 27 Aug 2021 14:28:28 +0200
Subject: gnu: Add python-pybbi.

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

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0979a86d8d..5d4b4e1316 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14795,6 +14795,53 @@ (define-public python-strawc
 data from @file{.hic} files.  This package provides Python bindings.")
     (license license:expat)))
 
+(define-public python-pybbi
+  (package
+    (name "python-pybbi")
+    (version "0.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pybbi" version))
+       (sha256
+        (base32
+         "1hvy2f28i2b41l1pq15vciqbj538n0lichp8yr6413jmgg06xdsk"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #false ; tests require network access
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'set-cc
+           (lambda _ (setenv "CC" "gcc")))
+         (replace 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (when tests?
+               (add-installed-pythonpath inputs outputs)
+               (copy-recursively "tests" "/tmp/tests")
+               (with-directory-excursion "/tmp/tests"
+                 (invoke "python" "-m" "pytest" "-v"))))))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("python-pkgconfig" ,python-pkgconfig)
+       ("python-pytest" ,python-pytest)))
+    (inputs
+     `(("libpng" ,libpng)
+       ("openssl" ,openssl)
+       ("zlib" ,zlib)))
+    (propagated-inputs
+     `(("python-cython" ,python-cython)
+       ("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
+       ("python-six" ,python-six)))
+    (home-page "https://github.com/nvictus/pybbi")
+    (synopsis "Python bindings to UCSC Big Binary file library")
+    (description
+     "This package provides Python bindings to the UCSC Big
+Binary (bigWig/bigBed) file library.  This provides read-level access to local
+and remote bigWig and bigBed files but no write capabilitites.  The main
+feature is fast retrieval of range queries into numpy arrays.")
+    (license license:expat)))
+
 (define-public r-ascat
   (package
    (name "r-ascat")
-- 
cgit v1.2.3


From d84ead81743cc76778241c73ac02c8c6c7e8f7ce Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 27 Aug 2021 14:30:04 +0200
Subject: gnu: Add python-dna-features-viewer.

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

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5d4b4e1316..1974978700 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14842,6 +14842,30 @@ (define-public python-pybbi
 feature is fast retrieval of range queries into numpy arrays.")
     (license license:expat)))
 
+(define-public python-dna-features-viewer
+  (package
+    (name "python-dna-features-viewer")
+    (version "3.0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "dna_features_viewer" version))
+       (sha256
+        (base32
+         "0vci6kg2id6r6rh3cifq7ccnh7j0mb8iqg3hji6rva0ayrdqzafc"))))
+    (build-system python-build-system)
+    (arguments '(#:tests? #false)) ; there are none
+    (propagated-inputs
+     `(("python-biopython" ,python-biopython)
+       ("python-matplotlib" ,python-matplotlib)))
+    (home-page
+     "https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer")
+    (synopsis "Plot features from DNA sequences")
+    (description
+     "DNA Features Viewer is a Python library to visualize DNA features,
+e.g. from GenBank or Gff files, or Biopython SeqRecords.")
+    (license license:expat)))
+
 (define-public r-ascat
   (package
    (name "r-ascat")
-- 
cgit v1.2.3


From b105655670636789524a375729010035972f5330 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 30 Aug 2021 18:25:09 +0200
Subject: gnu: python-scanpy: Update to 1.8.1.

* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.8.1.
[arguments]: Bulid with flit; update list of broken tests.
[native-inputs]: Add python-flit and python-anndata:source.
---
 gnu/packages/bioinformatics.scm | 63 +++++++++++++++++++++++++++++++----------
 1 file changed, 48 insertions(+), 15 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1974978700..ac918eac8f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11452,38 +11452,53 @@ (define-public fit-sne
 (define-public python-scanpy
   (package
     (name "python-scanpy")
-    (version "1.7.2")
+    (version "1.8.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "scanpy" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/theislab/scanpy")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0c66adnfizsyk0h8bv2yhmay876z0klpxwpn4z6m71wly7yplpmd"))))
+         "0w1qmv3djqi8q0sn5hv34ivzs157fwjjb9nflfnagnhpxmw8vx5g"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
+         (replace 'build
+           (lambda _
+             (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" ,version)
+             ;; ZIP does not support timestamps before 1980.
+             (setenv "SOURCE_DATE_EPOCH" "315532800")
+             (invoke "flit" "build")))
+         (replace 'install
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (add-installed-pythonpath inputs outputs)
+             (let ((out (assoc-ref outputs "out")))
+               (for-each (lambda (wheel)
+                           (format #true wheel)
+                           (invoke "python" "-m" "pip" "install"
+                                   wheel (string-append "--prefix=" out)))
+                         (find-files "dist" "\\.whl$")))))
          (replace 'check
            (lambda* (#:key inputs #:allow-other-keys)
              ;; These tests require Internet access.
              (delete-file-recursively "scanpy/tests/notebooks")
              (delete-file "scanpy/tests/test_clustering.py")
              (delete-file "scanpy/tests/test_datasets.py")
+             (delete-file "scanpy/tests/test_score_genes.py")
              (delete-file "scanpy/tests/test_highly_variable_genes.py")
 
              ;; TODO: I can't get the plotting tests to work, even with Xvfb.
-             (delete-file "scanpy/tests/test_plotting.py")
+             (delete-file "scanpy/tests/test_embedding_plots.py")
              (delete-file "scanpy/tests/test_preprocessing.py")
              (delete-file "scanpy/tests/test_read_10x.py")
 
-             ;; The following tests need anndata.tests, which aren't included
-             ;; in the final python-anndata package.
-             (delete-file "scanpy/tests/test_combat.py")
-             (delete-file "scanpy/tests/test_embedding_plots.py")
-             (delete-file "scanpy/tests/test_normalization.py")
-             (delete-file "scanpy/tests/test_pca.py")
-             (delete-file "scanpy/tests/external/test_scrublet.py")
+             ;; TODO: these fail with TypingError and "Use of unsupported
+             ;; NumPy function 'numpy.split'".
+             (delete-file "scanpy/tests/test_metrics.py")
 
              ;; The following tests requires 'scanorama', which isn't
              ;; packaged yet.
@@ -11491,9 +11506,24 @@ (define-public python-scanpy
 
              (setenv "PYTHONPATH"
                      (string-append (getcwd) ":"
+                                    (assoc-ref inputs "python-anndata:source") ":"
                                     (getenv "PYTHONPATH")))
-             (invoke "pytest")
-             #t)))))
+             (invoke "pytest" "-vv"
+                     "-k"
+                     ;; Plot tests that fail.
+                     (string-append "not test_dotplot_matrixplot_stacked_violin"
+                                    " and not test_violin_without_raw"
+                                    " and not test_correlation"
+                                    " and not test_scatterplots"
+                                    " and not test_scatter_embedding_add_outline_vmin_vmax_norm"
+                                    " and not test_paga"
+                                    " and not test_paga_compare"
+
+                                    ;; These try to connect to the network
+                                    " and not test_plot_rank_genes_groups_gene_symbols"
+                                    " and not test_pca_chunked"
+                                    " and not test_pca_sparse"
+                                    " and not test_pca_reproducible")))))))
     (propagated-inputs
      `(("python-anndata" ,python-anndata)
        ("python-h5py" ,python-h5py)
@@ -11517,7 +11547,10 @@ (define-public python-scanpy
        ("python-tqdm" ,python-tqdm)
        ("python-umap-learn" ,python-umap-learn)))
     (native-inputs
-     `(("python-leidenalg" ,python-leidenalg)
+     `(;; This package needs anndata.tests, which is not installed.
+       ("python-anndata:source" ,(package-source python-anndata))
+       ("python-flit" ,python-flit)
+       ("python-leidenalg" ,python-leidenalg)
        ("python-pytest" ,python-pytest)
        ("python-setuptools-scm" ,python-setuptools-scm)
        ("python-sinfo" ,python-sinfo)))
-- 
cgit v1.2.3


From 7712154ccb115e7d8d5b040fb45109369e42bc4b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 30 Aug 2021 18:29:25 +0200
Subject: gnu: Add python-coolbox.

* gnu/packages/bioinformatics.scm (python-coolbox): New variable.
---
 gnu/packages/bioinformatics.scm | 49 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ac918eac8f..eef22b8041 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -103,6 +103,7 @@ (define-module (gnu packages bioinformatics)
   #:use-module (gnu packages java)
   #:use-module (gnu packages java-compression)
   #:use-module (gnu packages jemalloc)
+  #:use-module (gnu packages jupyter)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages lisp-xyz)
   #:use-module (gnu packages logging)
@@ -14899,6 +14900,54 @@ (define-public python-dna-features-viewer
 e.g. from GenBank or Gff files, or Biopython SeqRecords.")
     (license license:expat)))
 
+(define-public python-coolbox
+  (package
+    (name "python-coolbox")
+    (version "0.3.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "coolbox" version))
+       (sha256
+        (base32
+         "0gqp76285w9klswr47y6kxbzwhv033b26jfa179kccfhiaq5p2xa"))))
+    (build-system python-build-system)
+    (arguments '(#:tests? #false)) ; there are none
+    (inputs
+     `(("pybind11" ,pybind11)))
+    (propagated-inputs
+     `(("python-cooler" ,python-cooler)
+       ("python-dna-features-viewer" ,python-dna-features-viewer)
+       ("python-fire" ,python-fire)
+       ("python-h5py" ,python-h5py)
+       ("python-intervaltree" ,python-intervaltree)
+       ("python-ipywidgets" ,python-ipywidgets)
+       ("jupyter" ,jupyter)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-nbformat" ,python-nbformat)
+       ("python-numpy" ,python-numpy)
+       ("python-numpydoc" ,python-numpydoc)
+       ("python-pandas" ,python-pandas)
+       ("python-pybbi" ,python-pybbi)
+       ("python-pytest" ,python-pytest)
+       ("python-scipy" ,python-scipy)
+       ("python-statsmodels" ,python-statsmodels)
+       ("python-strawc" ,python-strawc)
+       ("python-svgutils" ,python-svgutils)
+       ("python-termcolor" ,python-termcolor)
+       ("python-voila" ,python-voila)))
+    (home-page "https://github.com/GangCaoLab/CoolBox")
+    (synopsis "Genomic data visualization toolkit")
+    (description
+     "CoolBox is a toolkit for visual analysis of genomics data.  It aims to
+be highly compatible with the Python ecosystem, easy to use and highly
+customizable with a well-designed user interface.  It can be used in various
+visualization situations, for example, to produce high-quality genome track
+plots or fetch common used genomic data files with a Python script or command
+line, interactively explore genomic data within Jupyter environment or web
+browser.")
+    (license license:gpl3+)))
+
 (define-public r-ascat
   (package
    (name "r-ascat")
-- 
cgit v1.2.3


From 55cb5a62a1d27190f2241a4748a7a64d94715530 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 31 Aug 2021 23:04:49 +0200
Subject: gnu: python-scanpy: Propagate sinfo.

* gnu/packages/bioinformatics.scm (python-scanpy)[native-inputs]: Move
python-sinfo from here...
[propagated-inputs]: ...to here.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index eef22b8041..6fde9a474e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11542,6 +11542,7 @@ (define-public python-scanpy
        ("python-scikit-learn" ,python-scikit-learn)
        ("python-scipy" ,python-scipy)
        ("python-seaborn" ,python-seaborn)
+       ("python-sinfo" ,python-sinfo)
        ("python-statsmodels" ,python-statsmodels)
        ("python-tables" ,python-tables)
        ("python-pytoml" ,python-pytoml)
@@ -11553,8 +11554,7 @@ (define-public python-scanpy
        ("python-flit" ,python-flit)
        ("python-leidenalg" ,python-leidenalg)
        ("python-pytest" ,python-pytest)
-       ("python-setuptools-scm" ,python-setuptools-scm)
-       ("python-sinfo" ,python-sinfo)))
+       ("python-setuptools-scm" ,python-setuptools-scm)))
     (home-page "https://github.com/theislab/scanpy")
     (synopsis "Single-Cell Analysis in Python.")
     (description "Scanpy is a scalable toolkit for analyzing single-cell gene
-- 
cgit v1.2.3


From a1ee2121843d2b7eea2dc932f16d543ae7ff7007 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 31 Aug 2021 23:05:53 +0200
Subject: gnu: python-strawc: Propagate pybind11.

* gnu/packages/bioinformatics.scm (python-strawc)[inputs]: Move pybind11 from
here...
[propagated-inputs]: ...to here.
---
 gnu/packages/bioinformatics.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6fde9a474e..c199883829 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14821,8 +14821,9 @@ (define-public python-strawc
     (build-system python-build-system)
     (inputs
      `(("curl" ,curl)
-       ("pybind11" ,pybind11)
        ("zlib" ,zlib)))
+    (propagated-inputs
+     `(("pybind11" ,pybind11)))
     (home-page "https://github.com/aidenlab/straw")
     (synopsis "Stream data from .hic files")
     (description "Straw is library which allows rapid streaming of contact
-- 
cgit v1.2.3


From 4abf2268338f34fc85a24e14a3bbcc6803fa0e82 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 31 Aug 2021 23:10:42 +0200
Subject: gnu: Add scregseg.

* gnu/packages/bioinformatics.scm (scregseg): New variable.
---
 gnu/packages/bioinformatics.scm | 50 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c199883829..aef9625534 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14949,6 +14949,56 @@ (define-public python-coolbox
 browser.")
     (license license:gpl3+)))
 
+(define-public scregseg
+  (package
+    (name "scregseg")
+    (version "0.1.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/BIMSBbioinfo/scregseg")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1k8hllr5if6k2mm2zj391fv40sfc008cjm04l9vgfsdppb80i112"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #false                  ; tests require network access
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'do-not-fail-to-find-sklearn
+           (lambda _
+             ;; XXX: I have no idea why it cannot seem to find sklearn.
+             (substitute* "setup.py"
+               (("'sklearn',") "")))))))
+    (native-inputs
+     `(("python-cython" ,python-cython)))
+    (propagated-inputs
+     `(("python-scikit-learn" ,python-scikit-learn)
+       ("python-scipy" ,python-scipy)
+       ("python-numpy" ,python-numpy)
+       ("python-hmmlearn" ,python-hmmlearn)
+       ("python-pandas" ,python-pandas)
+       ("python-numba" ,python-numba)
+       ("python-anndata" ,python-anndata)
+       ("python-scanpy" ,python-scanpy)
+       ("python-pybedtools" ,python-pybedtools)
+       ("python-pysam" ,python-pysam)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-seaborn" ,python-seaborn)
+       ("python-coolbox" ,python-coolbox)))
+    (home-page "https://github.com/BIMSBbioinfo/scregseg")
+    (synopsis "Single-cell regulatory landscape segmentation")
+    (description "Scregseg (Single-Cell REGulatory landscape SEGmentation) is a
+tool that facilitates the analysis of single cell ATAC-seq data by an
+HMM-based segmentation algorithm.  Scregseg uses an HMM with
+Dirichlet-Multinomial emission probabilities to segment the genome either
+according to distinct relative cross-cell accessibility profiles or (after
+collapsing the single-cell tracks to pseudo-bulk tracks) to capture distinct
+cross-cluster accessibility profiles.")
+    (license license:gpl3+)))
+
 (define-public r-ascat
   (package
    (name "r-ascat")
-- 
cgit v1.2.3


From c75b30d58f0becb0a5cd6a8bfe69d1063b0d1ada Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 1 Sep 2021 14:52:12 +0200
Subject: gnu: Add r-catch.

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

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index aef9625534..b74d8925db 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15058,6 +15058,34 @@ (define-public r-battenberg
 @url{doi:10.1016/j.cell.2012.04.023,Nik-Zainal et al.}")
    (license license:gpl3)))
 
+(define-public r-catch
+  (let ((commit "196ddd5a51b1a5f5daa01de53fdaad9b7505e084")
+        (revision "1"))
+    (package
+      (name "r-catch")
+      (version (git-version "1.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/zhanyinx/CaTCH")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "11c7f1fc8f57wnwk1hrgr5y814m80zj8gkz5021vxyxy2v02cqgd"))))
+      (build-system r-build-system)
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'chdir
+             (lambda _ (chdir "CaTCH"))))))
+      (home-page "https://github.com/zhanyinx/CaTCH_R")
+      (synopsis "Call a hierarchy of domains based on Hi-C data")
+      (description "This package allows building the hierarchy of domains
+starting from Hi-C data.  Each hierarchical level is identified by a minimum
+value of physical insulation between neighboring domains.")
+      (license license:gpl2+))))
+
 (define-public r-spectre
   (let ((commit "f6648ab3eb9499300d86502b5d60ec370ae9b61a")
         (revision "1"))
-- 
cgit v1.2.3


From c82b723bf8f62718f3448869170cf963249e88c5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 6 Sep 2021 14:40:19 +0200
Subject: gnu: Add megadepth.

* gnu/packages/bioinformatics.scm (megadepth): New variable.
---
 gnu/packages/bioinformatics.scm | 65 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 65 insertions(+)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b74d8925db..c3ab0ce354 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14999,6 +14999,71 @@ (define-public scregseg
 cross-cluster accessibility profiles.")
     (license license:gpl3+)))
 
+(define-public megadepth
+  (package
+    (name "megadepth")
+    (version "1.1.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/ChristopherWilks/megadepth")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0hj69d2dgmk2zwgazik7xzc04fxxlk93p888kpgc52fmhd95qph7"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #false ; some tests seem to require connection to
+                       ; www.ebi.ac.uk; this may be caused by htslib.
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'prepare-CMakeLists.txt
+           (lambda _
+             (rename-file "CMakeLists.txt.ci" "CMakeLists.txt")
+             (substitute* "CMakeLists.txt"
+               (("`cat ../VERSION`") ,version)
+               (("target_link_libraries\\(megadepth_static") "#")
+               (("target_link_libraries\\(megadepth_statlib") "#")
+               (("add_executable\\(megadepth_static") "#")
+               (("add_executable\\(megadepth_statlib") "#"))
+
+             (substitute* "tests/test.sh"
+               ;; Disable remote test
+               (("./megadepth http://stingray.cs.jhu.edu/data/temp/test.bam") "#")
+               ;; Prior to installation the binary's name differs from what
+               ;; the test script assumes.
+               (("./megadepth") "../build/megadepth_dynamic"))))
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (with-directory-excursion "../source"
+                 (invoke "bash" "tests/test.sh" "use-local-test-data")))))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+               (mkdir-p bin)
+               (copy-file "megadepth_dynamic"
+                          (string-append bin "/megadepth"))))))))
+    (native-inputs
+     `(("diffutils" ,diffutils)
+       ("perl" ,perl)
+       ("grep" ,grep)))
+    (inputs
+     `(("curl" ,curl)
+       ("htslib" ,htslib)
+       ("libdeflate" ,libdeflate)
+       ("libbigwig" ,libbigwig)
+       ("zlib" ,zlib)))
+    (home-page "https://github.com/ChristopherWilks/megadepth")
+    (synopsis "BigWig and BAM/CRAM related utilities")
+    (description "Megadepth is an efficient tool for extracting coverage
+related information from RNA and DNA-seq BAM and BigWig files.  It supports
+reading whole-genome coverage from BAM files and writing either indexed TSV or
+BigWig files, as well as efficient region coverage summary over intervals from
+both types of files.")
+    (license license:expat)))
+
 (define-public r-ascat
   (package
    (name "r-ascat")
-- 
cgit v1.2.3