Merge branch 'master' into gnome-team

1 files changed, 398 insertions, 18 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2e4bc876d4..7dbebcf3da 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -130,6 +130,7 @@
   #:use-module (gnu packages pdf)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages perl-check)
+  #:use-module (gnu packages perl-web)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages popt)
   #:use-module (gnu packages protobuf)
@@ -574,6 +575,30 @@ BED, GFF/GTF, VCF.")
 whole-genome bisulfite sequencing (WGBS) reads from directional protocol.")
     (license license:asl2.0)))
 
+(define-public bustools
+  (package
+    (name "bustools")
+    (version "0.43.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/BUStools/bustools")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "068kjlc4d528269nl5mc3j8h2c95r1v545d3fi1iw1ckg8rba0hg"))))
+    (build-system cmake-build-system)
+    (arguments (list #:tests? #f))          ;no test target
+    (inputs (list zlib))
+    (home-page "https://bustools.github.io")
+    (synopsis "Tools for working with BUS files")
+    (description "bustools is a program for manipulating BUS files for single
+cell RNA-Seq datasets.  It can be used to error correct barcodes, collapse
+UMIs, produce gene count or transcript compatibility count matrices, and is useful
+for many other tasks.")
+    (license license:bsd-2)))
+
 (define-public cellsnp-lite
   ;; Last release is from November 2021 and does not contain fixes.
   (let ((commit "0885d746b0b1ea65c8ef92f8943ca7669ca9734a")
@@ -617,6 +642,50 @@ Compared to cellSNP, this package is more efficient with higher speed and less
 memory usage.")
       (license license:asl2.0))))
 
+(define-public cpat
+  (package
+    (name "cpat")
+    (version "3.0.4")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "CPAT" version))
+              (sha256
+               (base32
+                "0dfrwwbhv1n4nh2a903d1qfb30fgxgya89sa70aci3wzf8h2z0vd"))
+              (modules '((guix build utils)))
+              (snippet
+               '(for-each delete-file-recursively
+                          (list ".eggs"
+                                "lib/__pycache__/"
+                                "lib/cpmodule/__pycache__/")))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (with-directory-excursion "test"
+                 ;; There is no test4.fa
+                 (substitute* "test.sh"
+                   ((".*-g test4.fa.*") ""))
+                 (invoke "bash" "test.sh"))))))))
+    (propagated-inputs
+     (list python-numpy python-pysam))
+    (inputs
+     (list r-minimal))
+    (home-page "https://wlcb.oit.uci.edu/cpat/")
+    (synopsis "Alignment-free distinction between coding and noncoding RNA")
+    (description
+     "CPAT is a method to distinguish coding and noncoding RNA by using a
+logistic regression model based on four pure sequence-based, linguistic
+features: ORF size, ORF coverage, Ficket TESTCODE, and Hexamer usage bias.
+Linguistic features based method does not require other genomes or protein
+databases to perform alignment and is more robust.  Because it is
+alignment-free, it runs much faster and also easier to use.")
+    (license license:gpl2+)))
+
 (define-public pbcopper
   (package
     (name "pbcopper")
@@ -1070,6 +1139,42 @@ of single-cell data using Seurat, RcppML nmf, SingleCellExperiments and
 similar.")
       (license license:gpl2+))))
 
+(define-public r-stacas
+  (package
+    (name "r-stacas")
+    (version "2.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/carmonalab/STACAS")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "13i0h5i6vlbrb8ndq9gr81560z9d74b2c7m3rjfzls01irjza9hm"))))
+    (properties `((upstream-name . "STACAS")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocneighbors
+           r-biocparallel
+           r-ggplot2
+           r-ggridges
+           r-pbapply
+           r-r-utils
+           r-seurat))
+    (home-page "https://github.com/carmonalab/STACAS")
+    (synopsis "Sub-type anchoring correction for alignment in Seurat")
+    (description
+     "This package implements methods for batch correction and integration of
+scRNA-seq datasets, based on the Seurat anchor-based integration framework.
+In particular, STACAS is optimized for the integration of heterogenous
+datasets with only limited overlap between cell sub-types (e.g. TIL sets of
+CD8 from tumor with CD8/CD4 T cells from lymphnode), for which the default
+Seurat alignment methods would tend to over-correct biological differences.
+The 2.0 version of the package allows the users to incorporate explicit
+information about cell-types in order to assist the integration process.")
+    (license license:gpl3)))
+
 (define-public r-stringendo
   (let ((commit "15594b1bba11048a812874bafec0eea1dcc8618a")
         (revision "1"))
@@ -1156,6 +1261,32 @@ shape.  This package provides an @code{htmlwidget} for building streamgraph
 visualizations.")
       (license license:expat))))
 
+(define-public r-wasabi
+  (let ((commit "8c33cabde8d18c2657cd6e38e7cb834f87cf9846")
+        (revision "1"))
+    (package
+      (name "r-wasabi")
+      (version (git-version "1.0.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/COMBINE-lab/wasabi")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0rpdj6n4cnx8n2zl60dzgl638474sg49dknwi9x3qb4g56dpphfa"))))
+      (properties `((upstream-name . "wasabi")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-data-table r-rhdf5 r-rjson))
+      (home-page "https://github.com/COMBINE-lab/wasabi")
+      (synopsis "Use Sailfish and Salmon with Sleuth")
+      (description
+       "This package converts the output of the Sailfish and Salmon RNA-seq
+quantification tools so that it can be used with the Sleuth differential
+analysis package.")
+      (license license:bsd-3))))
+
 (define-public pbbam
   (package
     (name "pbbam")
@@ -2259,6 +2390,40 @@ sequencing data and the end result are tables of UMI-unique DamID and CEL-Seq
 counts.")
     (license license:expat)))
 
+(define-public python-snaptools
+  (package
+    (name "python-snaptools")
+    (version "1.4.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "snaptools" version))
+       (sha256
+        (base32
+         "1s5373g5jjbshh3q39zy7dlxr7nda6ksxq9d1gw46h82c4fsmfbn"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+     (list python-future
+           python-h5py
+           python-louvain
+           python-numpy
+           python-pybedtools
+           python-pysam))
+    (home-page "https://github.com/r3fang/SnapTools")
+    (synopsis "Tools for processing snap files" )
+    (description
+     "@code{SnapTools} can operate on snap files the following types of
+operations:
+
+@itemize
+@item index the reference genome before alignment;
+@item align reads to the corresponding reference genome;
+@item pre-process by convert pair-end reads into fragments, checking the
+  mapping quality score, alingment and filtration;
+@item create the cell-by-bin matrix.
+@end itemize")
+    (license license:asl2.0)))
+
 (define-public python-bioframe
   (package
     (name "python-bioframe")
@@ -4893,6 +5058,126 @@ be of arbitrary length. Repeats with pattern size in the range from 1 to 2000
 bases are detected.")
     (license license:agpl3+)))
 
+(define-public trinityrnaseq
+  (package
+    (name "trinityrnaseq")
+    (version "2.13.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/trinityrnaseq/trinityrnaseq.git")
+                    (commit (string-append "Trinity-v" version))
+                    (recursive? #true)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1qszrxqbx4q5pavpgm4rkrh1z1v1mf7qx83vv3fnlqdmncnsf1gv"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:test-target "test"
+      #:modules
+      '((guix build gnu-build-system)
+        (guix build utils)
+        (ice-9 match)
+        (srfi srfi-1))
+      #:make-flags
+      #~(list (string-append "CC=" #$(cc-for-target)))
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'configure
+            (lambda _
+              (setenv "SHELL" (which "sh"))
+              (setenv "CONFIG_SHELL" (which "sh"))
+              ;; Do not require version.h, which triggers a local build of a
+              ;; vendored htslib.
+              (substitute* "trinity-plugins/bamsifter/Makefile"
+                (("sift_bam_max_cov.cpp htslib/version.h")
+                 "sift_bam_max_cov.cpp"))))
+          (add-after 'build 'build-plugins
+            (lambda _
+              ;; Run this in the subdirectory to avoid running the
+              ;; tests right here.
+              (with-directory-excursion "trinity-plugins"
+                (invoke "make" "plugins"))))
+          ;; The install script uses rsync, provides no overrides for the
+          ;; default location at /usr/local/bin, and patching it would change
+          ;; all lines that do something.
+          (replace 'install
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let ((share (string-append #$output "/share/trinity/"))
+                    (bin   (string-append #$output "/bin/")))
+                (mkdir-p bin)
+                (copy-recursively "." share)
+                (delete-file (string-append share "/Chrysalis/build/CMakeFiles/CMakeOutput.log"))
+                (delete-file (string-append share "/Inchworm/build/CMakeFiles/CMakeOutput.log"))
+
+                (wrap-program (string-append share "Trinity")
+                  `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
+                  `("PERL5LIB"    ":" = (,(getenv "PERL5LIB")))
+                  `("PYTHONPATH"  ":" = (,(getenv "GUIX_PYTHONPATH")))
+                  `("PATH"        ":" =
+                    ,(cons (string-append share "/trinity-plugins/BIN")
+                           (filter-map (match-lambda
+                                         ((name . dir)
+                                          (string-append dir "/bin")))
+                                       inputs))))
+                (symlink (string-append share "Trinity")
+                         (string-append bin "Trinity"))))))))
+    (inputs
+     (list blast+
+           bowtie
+           fastqc
+           hisat
+           htslib
+           icedtea-8
+           jellyfish
+           kallisto
+           multiqc
+           perl
+           perl-uri-escape
+           python-numpy
+           python-wrapper
+           r-ape
+           r-argparse
+           r-biobase
+           r-ctc
+           r-deseq2
+           r-edger
+           r-fastcluster
+           r-glimma
+           r-goplot
+           r-goseq
+           r-gplots
+           r-minimal
+           r-qvalue
+           r-rots
+           r-sm
+           r-tidyverse
+           rsem
+           salmon
+           samtools
+           sra-tools
+           star
+           zlib))
+    (propagated-inputs
+     (list coreutils
+           gzip
+           which))
+    (native-inputs (list cmake))
+    (home-page "https://github.com/trinityrnaseq/trinityrnaseq/wiki")
+    (synopsis "Trinity RNA-Seq de novo transcriptome assembly")
+    (description "Trinity assembles transcript sequences from Illumina RNA-Seq
+data.  Trinity represents a novel method for the efficient and robust de novo
+reconstruction of transcriptomes from RNA-seq data.  Trinity combines three
+independent software modules: Inchworm, Chrysalis, and Butterfly, applied
+sequentially to process large volumes of RNA-seq reads.  Trinity partitions
+the sequence data into many individual de Bruijn graphs, each representing the
+transcriptional complexity at a given gene or locus, and then processes each
+graph independently to extract full-length splicing isoforms and to tease
+apart transcripts derived from paralogous genes.")
+    (license license:bsd-3)))
+
 (define-public repeat-masker
   (package
     (name "repeat-masker")
@@ -10313,6 +10598,51 @@ data.  This package includes panel editing or renaming for FCS files,
 bead-based normalization and debarcoding.")
       (license license:gpl3))))
 
+(define-public r-projectils
+  (let ((commit "cc73b97471b4b6eea11ce779b5c4a7dc5c3e1709")
+        (revision "1"))
+    (package
+      (name "r-projectils")
+      (version (git-version "3.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/carmonalab/ProjecTILs")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0dpzvbhhb9andnj7angpj32cgkwd6rs6qgpl6i21pqzcn6vqqhqw"))))
+      (properties `((upstream-name . "ProjecTILs")))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-biocneighbors
+             r-biocparallel
+             r-dplyr
+             r-ggplot2
+             r-matrix
+             r-patchwork
+             r-pheatmap
+             r-pracma
+             r-purrr
+             r-rcolorbrewer
+             r-reshape2
+             r-scales
+             r-scgate
+             r-seurat
+             r-seuratobject
+             r-stacas
+             r-ucell
+             r-umap
+             r-uwot))
+      (home-page "https://github.com/carmonalab/ProjecTILs")
+      (synopsis "Reference-based analysis of scRNA-seq data")
+      (description
+       "This package implements methods to project single-cell RNA-seq data
+onto a reference atlas, enabling interpretation of unknown cell transcriptomic
+states in the the context of known, reference states.")
+      (license license:gpl3))))
+
 (define-public r-presto
   (let ((commit "052085db9c88aa70a28d11cc58ebc807999bf0ad")
         (revision "0"))
@@ -10527,6 +10857,43 @@ analysis of cell types, subtypes, transcriptional gradients,cell-cycle
 variation, gene modules and their regulatory models and more.")
       (license license:expat))))
 
+(define-public r-sleuth
+  (package
+    (name "r-sleuth")
+    (version "0.30.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/pachterlab/sleuth")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "09xgc7r6iisjkk0c0wn0q56zy0aph386kphwixfzq4422y7vlqci"))))
+    (properties `((upstream-name . "sleuth")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-aggregation
+                             r-data-table
+                             r-dplyr
+                             r-ggplot2
+                             r-lazyeval
+                             r-matrixstats
+                             r-pheatmap
+                             r-reshape2
+                             r-rhdf5
+                             r-shiny
+                             r-tidyr))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/pachterlab/sleuth")
+    (synopsis "Tools for investigating RNA-Seq")
+    (description
+     "Sleuth is a program for differential analysis of RNA-Seq data.
+It makes use of quantification uncertainty estimates obtained via Kallisto for
+accurate differential analysis of isoforms or genes, allows testing in the
+context of experiments with complex designs, and supports interactive
+exploratory data analysis via sleuth live.")
+    (license license:gpl3)))
+
 (define-public r-snapatac
   (package
     (name "r-snapatac")
@@ -16602,7 +16969,16 @@ the HiCExplorer and pyGenomeTracks packages.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1yavgxry38g326z10bclvdf8glmma05fxj5m73h15m1r2l9xmw3v"))))
+         "1yavgxry38g326z10bclvdf8glmma05fxj5m73h15m1r2l9xmw3v"))
+       (modules '((guix build utils)))
+       ;; setup.py is malformed. The requirements are defined using a catchall
+       ;; pattern for the patch version number. This has been fixed in version
+       ;; 3.7.3, but we cannot upgrade to this version yet, since some Guix
+       ;; packages are not new enough. (See upstream commit
+       ;; 4845c715ec7b105e938d0c2426e27d0181690bfe for the fix).
+       (snippet '(substitute* "setup.py"
+                   (("\\.\\*")
+                    "")))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -20324,24 +20700,28 @@ aligner.")
        (uri (pypi-uri "scvelo" version))
        (sha256
         (base32 "0h5ha1459ljs0qgpnlfsw592i8dxqn6p9bl08l1ikpwk36baxb7z"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         ;; Numba needs a writable dir to cache functions.
-         (add-before 'check 'set-numba-cache-dir
-           (lambda _
-             (setenv "NUMBA_CACHE_DIR" "/tmp")))
-         (replace 'check
-           (lambda* (#:key outputs tests? #:allow-other-keys)
-             (when tests?
-               ;; The discovered test file names must match the names of the
-               ;; compiled files, so we cannot run the tests from
-               ;; /tmp/guix-build-*.
-               (with-directory-excursion
-                   (string-append (assoc-ref outputs "out")
-                                  "/lib/python3.10/site-packages/scvelo/core/tests/")
-                 (invoke "pytest" "-v"))))))))
+     (list
+       #:test-flags
+       ;; XXX: these two tests fail for unknown reasons
+       '(list "-k" "not test_perfect_fit and not test_perfect_fit_2d")
+       #:phases
+       #~(modify-phases %standard-phases
+           ;; Numba needs a writable dir to cache functions.
+           (add-before 'check 'set-numba-cache-dir
+             (lambda _
+               (setenv "NUMBA_CACHE_DIR" "/tmp")))
+           (replace 'check
+             (lambda* (#:key tests? test-flags #:allow-other-keys)
+               (when tests?
+                 ;; The discovered test file names must match the names of the
+                 ;; compiled files, so we cannot run the tests from
+                 ;; /tmp/guix-build-*.
+                 (with-directory-excursion
+                     (string-append #$output
+                                    "/lib/python3.10/site-packages/scvelo/core/tests/")
+                   (apply invoke "pytest" "-v" test-flags))))))))
     (propagated-inputs
      (list python-anndata
            python-hnswlib