diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 468 |
1 files changed, 449 insertions, 19 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4c6db1da6b..02c65eb99a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8,7 +8,7 @@ ;;; Copyright © 2016, 2020, 2022 Marius Bakke <marius@gnu.org> ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> -;;; Copyright © 2017, 2021, 2022 Arun Isaac <arunisaac@systemreboot.net> +;;; Copyright © 2017, 2021, 2022, 2024 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> ;;; Copyright © 2018-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> @@ -1101,6 +1101,43 @@ high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib.") (license license:lgpl2.0+)))) +(define-public r-scenic + (let ((commit "cedf8490a634da550cea2c831544e5f7f14467d2") + (revision "1")) + (package + (name "r-scenic") + (version (git-version "1.3.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/aertslab/SCENIC") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "17ai0q260hdqbvm1km1s5dw93pgz4f546ycfii57jyy9m9jka7r0")))) + (properties `((upstream-name . "SCENIC"))) + (build-system r-build-system) + (propagated-inputs (list r-aucell + r-data-table + r-dynamictreecut + r-genie3 + r-ggrepel + r-mixtools + r-nmf + r-rcistarget + r-rtsne)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/aertslab/SCENIC") + (synopsis + "SCENIC (Single Cell rEgulatory Network Inference and Clustering)") + (description "SCENIC (Single-cell regulatory network inference and +clustering) is an R package to infer Gene Regulatory Networks and cell types +from single-cell RNA-seq data.") + ;; As of commit cedf8490a634da550cea2c831544e5f7f14467d2 the license is + ;; GPLv3. + (license license:gpl3)))) + (define-public r-singlet (let ((commit "765a6c45081807a1522f0e8983e2417822a36f36") (revision "1")) @@ -1471,6 +1508,39 @@ cpp.find_library('hdf5_cpp', dirs : '~a'), " "Blasr is a genomic sequence aligner for processing PacBio long reads.") (license license:bsd-3))) +(define-public randfold + (package + (name "randfold") + (version "2.0.1") + (source + (origin + (method url-fetch) + (uri (string-append "http://bioinformatics.psb.ugent.be/" + "supplementary_data/erbon/nov2003/downloads/" + "randfold-" version ".tar.gz")) + (sha256 + (base32 + "0gqixl4ncaibrxmn25d6lm2hrw4ml2fj13nrc9q1kilsxdfi91mj")))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #f ;no tests provided + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda _ + (install-file "randfold" + (string-append #$output "/bin"))))))) + (inputs (list eddylab-squid)) + (home-page + "http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/") + (synopsis "Minimum free energy of folding randomization test software") + (description "randfold computes the probability that, for a given +sequence, the @dfn{Minimum Free Energy} (MFE) of the secondary structure is +different from MFE computed with random sequences.") + (license license:gpl2))) + (define-public ribotaper (package (name "ribotaper") @@ -2114,6 +2184,45 @@ matplotlib Axes objects, making them easy to style and incorporate into multi-panel figures.") (license license:expat))) +(define-public python-magic-impute + (package + (name "python-magic-impute") + (version "1.2.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/KrishnaswamyLab/MAGIC") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1yjs16vg87lcg9g16bnblg1v9sk73j6dm229lkcz0bfjlzxjhv8w")))) + (build-system pyproject-build-system) + (arguments + (list + #:tests? #false ;there are none + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ (chdir "python")))))) + (propagated-inputs + (list python-future + python-graphtools + python-matplotlib + python-numpy + python-pandas + python-scikit-learn + python-scipy + python-tasklogger)) + (home-page "https://github.com/KrishnaswamyLab/MAGIC") + (synopsis "Markov affinity-based graph imputation of cells") + (description "MAGIC is an interactive tool to impute missing values in +single-cell sequencing data and to restore the structure of the data. It also +provides data pre-processing functionality such as dimensionality reduction +and gene expression visualization.") + (license license:gpl2+))) + (define-public python-parabam (package (name "python-parabam") @@ -2431,6 +2540,7 @@ counts.") (base32 "1s5373g5jjbshh3q39zy7dlxr7nda6ksxq9d1gw46h82c4fsmfbn")))) (build-system pyproject-build-system) + (arguments (list #:tests? #false)) ;there are none (propagated-inputs (list python-future python-h5py @@ -4653,6 +4763,64 @@ meso, or continuum scale.") files.") (license license:expat))) +(define-public lsgkm + (package + (name "lsgkm") + (version "0.1.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Dongwon-Lee/lsgkm.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0b3m94kndvimdfjaf1q2yhmsn7lm5s9v81c5xgfjcp6ig7mh3sa5")))) + (build-system gnu-build-system) + (arguments + (list + #:make-flags '(list "-C" "src") + #:tests? #false ;there are no executable tests + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda _ + (let ((bin (string-append #$output "/bin"))) + (for-each (lambda (file) + (install-file file bin)) + '("src/gkmtrain" + "src/gkmpredict")))))))) + (home-page "https://github.com/Dongwon-Lee/lsgkm") + (synopsis "Predict regulatory DNA elements in large-scale data") + (description "gkm-SVM, a sequence-based method for predicting regulatory +DNA elements, is a useful tool for studying gene regulatory mechanisms. +LS-GKM is an effort to improve the method. It offers much better scalability +and provides further advanced gapped k-mer based kernel functions. As a +result, LS-GKM achieves considerably higher accuracy than the original +gkm-SVM.") + (license license:gpl3+))) + +(define-public python-fcsparser + (package + (name "python-fcsparser") + (version "0.2.8") + (source + (origin + (method url-fetch) + (uri (pypi-uri "fcsparser" version)) + (sha256 + (base32 "1skk1k8phq9sj4ar0cnq8px89y3kcyh5zrbl6anz9wcdcyzkc16z")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-numpy python-pandas)) + (native-inputs (list python-poetry-core python-pytest)) + (home-page "https://github.com/eyurtsev/fcsparser") + (synopsis "Package for reading raw fcs files") + (description + "This package provides a Python package for reading raw fcs files") + (license license:expat))) + (define-public python-pybigwig (package (name "python-pybigwig") @@ -4687,17 +4855,89 @@ files.") accessing bigWig files.") (license license:expat))) +(define-public python-pyfasta + ;; The release on pypi does not contain the test data files. + (let ((commit "c2f0611c5311f1b1466f2d56560447898b4a8b03") + (revision "1")) + (package + (name "python-pyfasta") + (version (git-version "0.5.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/brentp/pyfasta") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0a189id3fbv88gssyk6adbmz2ll1mqpmyw8vxmx3fi955gvaq9j7")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'python3.10-compat + (lambda _ + (substitute* "pyfasta/__init__.py" + (("from fasta import") + "from pyfasta.fasta import") + (("from records import") + "from pyfasta.records import") + (("from split_fasta import") + "from pyfasta.split_fasta import") + (("in f.iteritems") + "in f.items")) + (substitute* "pyfasta/fasta.py" + (("from collections import Mapping") + "from collections.abc import Mapping") + (("from records import") + "from pyfasta.records import")) + (substitute* "pyfasta/records.py" + (("cPickle") "pickle") + (("\\(int, long\\)") + "(int, int)") + ;; XXX: it's not clear if this is really correct. + (("buffer\\(self\\)") + "memoryview(bytes(str(self), encoding='utf-8'))") + (("sys.maxint") "sys.maxsize")) + (substitute* "pyfasta/split_fasta.py" + (("from cStringIO import") + "from io import") + (("in lens.iteritems") "in lens.items")) + (substitute* "tests/test_all.py" + (("f.keys\\(\\)\\) == \\['a-extra'") + "list(f.keys())) == ['a-extra'") + (("f.iterkeys\\(\\)") "iter(f.keys())") + (("tests/data/" m) + (string-append (getcwd) "/" m)))))))) + (propagated-inputs (list python-numpy)) + (native-inputs (list python-nose)) + (home-page "https://github.com/brentp/pyfasta/") + (synopsis "Pythonic access to fasta sequence files") + (description + "This library provides fast, memory-efficient, pythonic (and +command-line) access to fasta sequence files. It stores a flattened version +of a fasta sequence file without spaces or headers and uses either a +@code{mmap} in numpy binary format or @code{fseek}/@code{fread} so the +sequence data is never read into memory. It saves a pickle (@code{.gdx}) of +the start and stop (for @code{fseek}/@code{mmap}) locations of each header in +the fasta file for internal use. + +Note that this package has been deprecated in favor of @code{pyfaidx}.") + (license license:expat)))) + (define-public python-schema-salad (package (name "python-schema-salad") (version "8.2.20211116214159") (source - (origin - (method url-fetch) - (uri (pypi-uri "schema-salad" version)) - (sha256 - (base32 - "005dh2y45x92zl8sf2sqjmfvcqr4hrz8dfckgkckv87003v7lwqc")))) + (origin + (method url-fetch) + (uri (pypi-uri "schema-salad" version)) + (sha256 + (base32 + "005dh2y45x92zl8sf2sqjmfvcqr4hrz8dfckgkckv87003v7lwqc")))) (build-system pyproject-build-system) (arguments `(#:phases @@ -5434,6 +5674,35 @@ quantitative phenotypes.") ;; license is the GPL. (license license:gpl3+))) +(define-public eddylab-squid + (package + (name "eddylab-squid") + (version "1.9g") + (source + (origin + (method url-fetch) + (uri (string-append "http://eddylab.org/software/squid/squid-" + version ".tar.gz")) + (sha256 + (base32 + "19ywv1h581a84yyjnp64gwww99vhgbxi8v4rl37xp92ag7l44brh")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'check 'set-perl-search-path + (lambda _ + ;; Work around "dotless @INC" build failure. + (setenv "PERL5LIB" + (string-append (getcwd) "/Testsuite:" + (getenv "PERL5LIB")))))))) + (inputs (list perl)) + (home-page "http://eddylab.org/software.html") + (synopsis "C function library for sequence analysis") + (description "SQUID is Sean Eddy's personal library of C functions +and utility programs for sequence analysis.") + (license license:gpl2))) + (define-public edirect (package (name "edirect") @@ -6073,6 +6342,43 @@ sequences to the genome---manipulating the sequences to produce better mapping results. The FASTX-Toolkit tools perform some of these preprocessing tasks.") (license license:agpl3+))) +(define-public flash + (package + (name "flash") + (version "1.2.11") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/flashpage/FLASH-" + version ".tar.gz")) + (sha256 + (base32 + "1b1ns9ghbcxy92xwa2a53ikqacvnyhvca0zfv0s7986xzvvscp38")))) + (build-system gnu-build-system) + (arguments + (list + #:make-flags #~(list (string-append "CC=" #$(cc-for-target))) + #:tests? #f ;no tests + #:phases + #~(modify-phases %standard-phases + ;; No configure script + (delete 'configure) + ;; No install target + (replace 'install + (lambda _ + (install-file "flash" + (string-append #$output "/bin"))))))) + (inputs (list zlib)) + (home-page "http://ccb.jhu.edu/software/FLASH/") + (synopsis "Merge paired-end nucleotide reads from NGS experiments") + (description "FLASH (Fast Length Adjustment of SHort reads) is a tool to +merge paired-end reads from next-generation sequencing experiments. FLASH is +designed to merge pairs of reads when the original DNA fragments are shorter +than twice the length of reads. The resulting longer reads can significantly +improve genome assemblies. They can also improve transcriptome assembly when +FLASH is used to merge RNA-seq data.") + (license license:gpl3+))) + (define-public flexbar (package (name "flexbar") @@ -7365,6 +7671,49 @@ to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility.") (license license:gpl2+))) +(define-public isolator + (let ((commit "24bafc0a102dce213bfc2b5b9744136ceadaba03") + (revision "1")) + (package + (name "isolator") + (version (git-version "0.0.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dcjones/isolator.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "12mbcfqhiggcjvzizf2ff7b05z31i47njcyzcivpw5j74pfbr3dv")))) + (build-system cmake-build-system) + (arguments + (list + #:tests? #f ;no check target + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'fix-std + (lambda _ + (substitute* '("src/summarize.cpp" + "src/shredder.cpp") + (("isnan") "std::isnan") + (("isinf") "std::isinf"))))))) + (inputs + (list boost hdf5 zlib)) + (home-page "https://github.com/dcjones/isolator") + (synopsis "Tools for the analysis of RNA-Seq experiments") + (description "Isolator analyzes RNA-Seq experiments. Isolator has a +particular focus on producing stable, consistent estimates. It implements a +full hierarchical Bayesian model of an entire RNA-Seq experiment. It saves +all the samples generated by the sampler, which can be processed to compute +posterior probabilities for arbitrarily complex questions, far beyond the +confines of pairwise tests. It aggressively corrects for technical effects, +such as random priming bias, GC-bias, 3' bias, and fragmentation effects. +Compared to other MCMC approaches, it is exceedingly efficient, though +generally slower than modern maximum likelihood approaches.") + (license license:expat)))) + (define-public jellyfish (package (name "jellyfish") @@ -7836,6 +8185,45 @@ probabilistic distances of genome abundance and tetranucleotide frequency.") (license (license:non-copyleft "file://license.txt" "See license.txt in the distribution.")))) +(define-public metal + (package + (name "metal") + (version "2011-03-25") + (source + (origin + (method url-fetch) + (uri (string-append "http://csg.sph.umich.edu/abecasis/Metal/" + "download/generic-metal-" version ".tar.gz")) + (sha256 + (base32 + "1bk00hc0xagmq0mabmbb8bykl75qd4kfyirba869h4x6hmn4a0f3")))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #f + #:make-flags + #~(list (string-append "INSTALLDIR=" #$output "/bin") "all") + #:phases + '(modify-phases %standard-phases + (replace 'configure + (lambda _ + (substitute* "Makefile" + (("^CFLAGS=") "CFLAGS=-std=c++11 "))))))) + (inputs (list zlib `(,zlib "static"))) + (home-page "http://csg.sph.umich.edu/abecasis/Metal/") + (synopsis "Facilitate meta-analysis of large datasets") + (description "METAL is a tool for meta-analysis genomewide association +scans. METAL can combine either test statistics and standard errors or +p-values across studies (taking sample size and direction of effect into +account). METAL analysis is a convenient alternative to a direct analysis of +merged data from multiple studies. It is especially appropriate when data +from the individual studies cannot be analyzed together because of differences +in ethnicity, phenotype distribution, gender or constraints in sharing of +individual level data imposed. Meta-analysis results in little or no loss of +efficiency compared to analysis of a combined dataset including data from all +individual studies.") + (license license:bsd-3))) + (define-public minced (package (name "minced") @@ -7928,6 +8316,41 @@ program for nucleotide and protein sequences.") ;; License information found in 'muscle -h' and usage.cpp. (license license:public-domain))) +(define-public music + (let ((commit "b1caecdb164b1ab80acccb9463abe2526a56f69f") + (revision "1")) + (package + (name "music") + (version (git-version "0.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/gersteinlab/MUSIC.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0arj300h8cpbya7y98g066xsxcg2a65h3y0qs250rlj072f1b4ia")))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #f ; no "check" target + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + ;; There is no "install" target. + (replace 'install + (lambda _ + (let ((bin (string-append #$output "/bin"))) + (install-file "bin/MUSIC" bin))))))) + (home-page "https://github.com/gersteinlab/MUSIC/") + (synopsis "Multiscale enrichment calling for ChIP-Seq datasets") + (description + "MUSIC is an algorithm for identification of enriched regions at +multiple scales in the read depth signals from ChIP-Seq experiments.") + ;; See https://github.com/gersteinlab/MUSIC/issues/6 + (license license:gpl2+)))) + (define-public newick-utils ;; There are no recent releases so we package from git. (let ((commit "da121155a977197cab9fbb15953ca1b40b11eb87")) @@ -21321,7 +21744,7 @@ single-cell data named @url{https://github.com/PMBio/cardelino, cardelino}.") (define-public ccwl (package (name "ccwl") - (version "0.2.0") + (version "0.3.0") (source (origin (method url-fetch) @@ -21329,7 +21752,7 @@ single-cell data named @url{https://github.com/PMBio/cardelino, cardelino}.") version ".tar.lz")) (sha256 (base32 - "1ar8rfz3zrksgygrv67zv77y8gfvvz54zcs546jn6j28y20basla")))) + "0za710mcn9di1njli3dk3660n3836ip8b4msb8f958498va95y7j")))) (build-system gnu-build-system) (arguments `(#:make-flags '("GUILE_AUTO_COMPILE=0") ; to prevent guild warnings @@ -21340,6 +21763,12 @@ single-cell data named @url{https://github.com/PMBio/cardelino, cardelino}.") ,@%default-gnu-imported-modules) #:phases (modify-phases %standard-phases + (add-after 'patch-source-shebangs 'patch-more-source-shebangs + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "scripts/ccwl" + (("^exec guile") + (string-append "exec " + (search-input-file inputs "/bin/guile")))))) (add-after 'install 'wrap (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out")) @@ -21403,15 +21832,18 @@ based on the pairwise alignment of hidden Markov models (HMMs).") (define-public wfmash (package (name "wfmash") - (version "0.10.5") + (version "0.12.5") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/wfmash/releases/download/v" - version "/wfmash-v" version ".tar.gz")) + ;; There are no release tarballs after version 0.10.5. + (method git-fetch) + (uri (git-reference + (url "https://github.com/waveygang/wfmash") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1jsvnnh14h3ir4l13qhmglhd25kzwvni9apgvr1lbikqwgrpkiq4")) + "1qh2chnwp7nqgp88afc4xzdkd21vh6cfqq73siqw7vc0qinqadm6")) (snippet #~(begin (use-modules (guix build utils)) @@ -21437,8 +21869,7 @@ based on the pairwise alignment of hidden Markov models (HMMs).") (let ((samtools (search-input-file inputs "/bin/samtools"))) ;; This is the easiest way to access the data ;; needed for the test suite. - (symlink (string-append "../wfmash-v" #$version "/data") - "data") + (symlink "../source/data" "data") (and ;; This test takes 60 minutes on riscv64-linux. #$@(if (not (target-riscv64?)) @@ -21530,8 +21961,7 @@ based on the pairwise alignment of hidden Markov models (HMMs).") (lambda _ (invoke "bin/wfmash" "data/reads.255bps.fa.gz" - "data/reads.255bps.fa.gz" - "-X" "-w" "16"))) + "-w" "16" "-s" "100" "-L"))) (invoke "head" "reads.255bps.paf")))))))))) (inputs (list atomic-queue @@ -21548,7 +21978,7 @@ distances and the wavefront alignment algorithm. It is a fork of MashMap that implements base-level alignment via the wflign tiled wavefront global alignment algorithm. It completes MashMap with a high-performance alignment module capable of computing base-level alignments for very large sequences.") - (home-page "https://github.com/ekg/wfmash") + (home-page "https://github.com/waveygang/wfmash") (license license:expat))) (define-public gdcm |