diff options
Diffstat (limited to 'pkgs/applications/science/biology')
55 files changed, 56 insertions, 56 deletions
diff --git a/pkgs/applications/science/biology/ants/default.nix b/pkgs/applications/science/biology/ants/default.nix index 6e1a2a3407ee1..20eedfaaa16c3 100644 --- a/pkgs/applications/science/biology/ants/default.nix +++ b/pkgs/applications/science/biology/ants/default.nix @@ -33,7 +33,7 @@ stdenv.mkDerivation rec { ''; meta = with stdenv.lib; { - homepage = https://github.com/ANTsX/ANTs; + homepage = "https://github.com/ANTsX/ANTs"; description = "Advanced normalization toolkit for medical image registration and other processing"; maintainers = with maintainers; [ bcdarwin ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/biology/aragorn/default.nix b/pkgs/applications/science/biology/aragorn/default.nix index a5f0ebc18abd6..956e4d884531c 100644 --- a/pkgs/applications/science/biology/aragorn/default.nix +++ b/pkgs/applications/science/biology/aragorn/default.nix @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Detects tRNA, mtRNA, and tmRNA genes in nucleotide sequences"; - homepage = http://mbio-serv2.mbioekol.lu.se/ARAGORN/; + homepage = "http://mbio-serv2.mbioekol.lu.se/ARAGORN/"; license = licenses.gpl2; maintainers = [ maintainers.bzizou ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix index 4a6a464de4648..b847fd8b5fe47 100644 --- a/pkgs/applications/science/biology/bcftools/default.nix +++ b/pkgs/applications/science/biology/bcftools/default.nix @@ -30,7 +30,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Tools for manipulating BCF2/VCF/gVCF format, SNP and short indel sequence variants"; license = licenses.mit; - homepage = http://www.htslib.org/; + homepage = "http://www.htslib.org/"; platforms = platforms.unix; maintainers = [ maintainers.mimame ]; }; diff --git a/pkgs/applications/science/biology/bedtools/default.nix b/pkgs/applications/science/biology/bedtools/default.nix index 9af2ec88c3921..332e06ea0cf5a 100644 --- a/pkgs/applications/science/biology/bedtools/default.nix +++ b/pkgs/applications/science/biology/bedtools/default.nix @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "A powerful toolset for genome arithmetic."; license = licenses.gpl2; - homepage = https://bedtools.readthedocs.io/en/latest/; + homepage = "https://bedtools.readthedocs.io/en/latest/"; maintainers = with maintainers; [ jbedo ]; platforms = platforms.unix; }; diff --git a/pkgs/applications/science/biology/bftools/default.nix b/pkgs/applications/science/biology/bftools/default.nix index 29e8bca52625a..2ecefee340fd6 100644 --- a/pkgs/applications/science/biology/bftools/default.nix +++ b/pkgs/applications/science/biology/bftools/default.nix @@ -35,7 +35,7 @@ stdenv.mkDerivation rec { description = "A bundle of scripts for using Bio-Formats on the command line with bioformats_package.jar already included"; license = licenses.gpl2; platforms = platforms.all; - homepage = https://www.openmicroscopy.org/bio-formats/; + homepage = "https://www.openmicroscopy.org/bio-formats/"; maintainers = [ maintainers.tbenst ]; }; } diff --git a/pkgs/applications/science/biology/blast/default.nix b/pkgs/applications/science/biology/blast/default.nix index ad737c6699d60..95a1b905e9e24 100644 --- a/pkgs/applications/science/biology/blast/default.nix +++ b/pkgs/applications/science/biology/blast/default.nix @@ -97,7 +97,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = ''Basic Local Alignment Search Tool (BLAST) finds regions of similarity between biological sequences''; - homepage = https://blast.ncbi.nlm.nih.gov/Blast.cgi; + homepage = "https://blast.ncbi.nlm.nih.gov/Blast.cgi"; license = licenses.publicDomain; # Version 2.10.0 fails on Darwin diff --git a/pkgs/applications/science/biology/bowtie2/default.nix b/pkgs/applications/science/biology/bowtie2/default.nix index 962428d67cf9c..dc818e2fb8684 100644 --- a/pkgs/applications/science/biology/bowtie2/default.nix +++ b/pkgs/applications/science/biology/bowtie2/default.nix @@ -18,7 +18,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences"; license = licenses.gpl3; - homepage = http://bowtie-bio.sf.net/bowtie2; + homepage = "http://bowtie-bio.sf.net/bowtie2"; maintainers = with maintainers; [ rybern ]; platforms = platforms.all; broken = stdenv.isAarch64; diff --git a/pkgs/applications/science/biology/bwa/default.nix b/pkgs/applications/science/biology/bwa/default.nix index 5e39320bf8355..e478c104edef9 100644 --- a/pkgs/applications/science/biology/bwa/default.nix +++ b/pkgs/applications/science/biology/bwa/default.nix @@ -18,7 +18,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "A software package for mapping low-divergent sequences against a large reference genome, such as the human genome"; license = licenses.gpl3; - homepage = http://bio-bwa.sourceforge.net/; + homepage = "http://bio-bwa.sourceforge.net/"; maintainers = with maintainers; [ luispedro ]; platforms = [ "x86_64-linux" ]; }; diff --git a/pkgs/applications/science/biology/cd-hit/default.nix b/pkgs/applications/science/biology/cd-hit/default.nix index 1a41a28a19aae..0db788b0f7431 100644 --- a/pkgs/applications/science/biology/cd-hit/default.nix +++ b/pkgs/applications/science/biology/cd-hit/default.nix @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { ''; meta = with stdenv.lib; { description = "Clustering and comparing protein or nucleotide sequences"; - homepage = http://weizhongli-lab.org/cd-hit/; + homepage = "http://weizhongli-lab.org/cd-hit/"; license = licenses.gpl2; maintainers = [ maintainers.bzizou ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/biology/clustal-omega/default.nix b/pkgs/applications/science/biology/clustal-omega/default.nix index 00acc25028c03..71cf879853767 100644 --- a/pkgs/applications/science/biology/clustal-omega/default.nix +++ b/pkgs/applications/science/biology/clustal-omega/default.nix @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "General purpose multiple sequence alignment program for protein and DNA/RNA"; - homepage = http://www.clustal.org/omega/; + homepage = "http://www.clustal.org/omega/"; license = licenses.gpl2; maintainers = [ maintainers.bzizou ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/biology/cmtk/default.nix b/pkgs/applications/science/biology/cmtk/default.nix index 1ebfa2fca57a1..41805c15aed59 100644 --- a/pkgs/applications/science/biology/cmtk/default.nix +++ b/pkgs/applications/science/biology/cmtk/default.nix @@ -21,6 +21,6 @@ stdenv.mkDerivation { maintainers = with maintainers; [ tbenst ]; platforms = platforms.all; license = licenses.gpl3; - homepage = https://www.nitrc.org/projects/cmtk/; + homepage = "https://www.nitrc.org/projects/cmtk/"; }; } diff --git a/pkgs/applications/science/biology/conglomerate/default.nix b/pkgs/applications/science/biology/conglomerate/default.nix index 23182fcadc6b5..971e2f23055b2 100644 --- a/pkgs/applications/science/biology/conglomerate/default.nix +++ b/pkgs/applications/science/biology/conglomerate/default.nix @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { ''; meta = with stdenv.lib; { - homepage = https://github.com/BIC-MNI/conglomerate; + homepage = "https://github.com/BIC-MNI/conglomerate"; description = "More command-line utilities for working with MINC files"; maintainers = with maintainers; [ bcdarwin ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/biology/dcm2niix/default.nix b/pkgs/applications/science/biology/dcm2niix/default.nix index 7c328034a3062..8ea3588fa8cac 100644 --- a/pkgs/applications/science/biology/dcm2niix/default.nix +++ b/pkgs/applications/science/biology/dcm2niix/default.nix @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format. ''; - homepage = https://www.nitrc.org/projects/dcm2nii; + homepage = "https://www.nitrc.org/projects/dcm2nii"; license = licenses.bsd3; maintainers = [ maintainers.ashgillman ]; platforms = platforms.all; diff --git a/pkgs/applications/science/biology/diamond/default.nix b/pkgs/applications/science/biology/diamond/default.nix index c1d20a11ca96a..dd1e13ec7162e 100644 --- a/pkgs/applications/science/biology/diamond/default.nix +++ b/pkgs/applications/science/biology/diamond/default.nix @@ -31,10 +31,10 @@ stdenv.mkDerivation { "Fast and sensitive protein alignment using DIAMOND", Nature Methods 12, 59-60 (2015). ''; - homepage = https://github.com/bbuchfink/diamond; + homepage = "https://github.com/bbuchfink/diamond"; license = { fullName = "University of Tuebingen, Benjamin Buchfink"; - url = https://raw.githubusercontent.com/bbuchfink/diamond/master/src/COPYING; + url = "https://raw.githubusercontent.com/bbuchfink/diamond/master/src/COPYING"; }; maintainers = [ maintainers.metabar ]; }; diff --git a/pkgs/applications/science/biology/ecopcr/default.nix b/pkgs/applications/science/biology/ecopcr/default.nix index 9e1b16ff94491..2e744c7b2b9ee 100644 --- a/pkgs/applications/science/biology/ecopcr/default.nix +++ b/pkgs/applications/science/biology/ecopcr/default.nix @@ -30,7 +30,7 @@ stdenv.mkDerivation rec { coverage and barcode specificity. New barcode primers can be developed using the ecoPrimers software. ''; - homepage = https://git.metabarcoding.org/obitools/ecopcr/wikis/home; + homepage = "https://git.metabarcoding.org/obitools/ecopcr/wikis/home"; license = licenses.cecill20; maintainers = [ maintainers.metabar ]; }; diff --git a/pkgs/applications/science/biology/eggnog-mapper/default.nix b/pkgs/applications/science/biology/eggnog-mapper/default.nix index e11f4ebf77c54..3ef52e543933b 100644 --- a/pkgs/applications/science/biology/eggnog-mapper/default.nix +++ b/pkgs/applications/science/biology/eggnog-mapper/default.nix @@ -33,7 +33,7 @@ python27Packages.buildPythonApplication rec { meta = with stdenv.lib; { description = "Fast genome-wide functional annotation through orthology assignment"; license = licenses.gpl2; - homepage = https://github.com/eggnogdb/eggnog-mapper/wiki; + homepage = "https://github.com/eggnogdb/eggnog-mapper/wiki"; maintainers = with maintainers; [ luispedro ]; platforms = platforms.all; }; diff --git a/pkgs/applications/science/biology/emboss/default.nix b/pkgs/applications/science/biology/emboss/default.nix index 2110a9bcfabab..e2374bcd1e2f8 100644 --- a/pkgs/applications/science/biology/emboss/default.nix +++ b/pkgs/applications/science/biology/emboss/default.nix @@ -23,6 +23,6 @@ stdenv.mkDerivation { data in a variety of formats and even allows transparent retrieval of sequence data from the web.''; license = "GPL2"; - homepage = http://emboss.sourceforge.net/; + homepage = "http://emboss.sourceforge.net/"; }; } diff --git a/pkgs/applications/science/biology/est-sfs/default.nix b/pkgs/applications/science/biology/est-sfs/default.nix index dcc7252335517..1b15c06c670a1 100644 --- a/pkgs/applications/science/biology/est-sfs/default.nix +++ b/pkgs/applications/science/biology/est-sfs/default.nix @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { ''; meta = with stdenv.lib; { - homepage = https://sourceforge.net/projects/est-usfs; + homepage = "https://sourceforge.net/projects/est-usfs"; description = "Estimate the unfolded site frequency spectrum and ancestral states"; license = licenses.gpl3; maintainers = [ maintainers.bzizou ]; diff --git a/pkgs/applications/science/biology/exonerate/default.nix b/pkgs/applications/science/biology/exonerate/default.nix index 1dd6b44692a38..b2c49ab007676 100644 --- a/pkgs/applications/science/biology/exonerate/default.nix +++ b/pkgs/applications/science/biology/exonerate/default.nix @@ -17,7 +17,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Generic tool for sequence alignment"; - homepage = https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate; + homepage = "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate"; license = licenses.gpl3; maintainers = [ maintainers.bzizou ]; platforms = platforms.unix ; diff --git a/pkgs/applications/science/biology/freebayes/default.nix b/pkgs/applications/science/biology/freebayes/default.nix index 7d0a36e755f62..bd80df56cb905 100644 --- a/pkgs/applications/science/biology/freebayes/default.nix +++ b/pkgs/applications/science/biology/freebayes/default.nix @@ -22,7 +22,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Bayesian haplotype-based polymorphism discovery and genotyping"; license = licenses.mit; - homepage = https://github.com/ekg/freebayes; + homepage = "https://github.com/ekg/freebayes"; maintainers = with maintainers; [ jdagilliland ]; platforms = [ "x86_64-linux" ]; }; diff --git a/pkgs/applications/science/biology/hisat2/default.nix b/pkgs/applications/science/biology/hisat2/default.nix index 824856301145b..fb7f2cba3de3b 100644 --- a/pkgs/applications/science/biology/hisat2/default.nix +++ b/pkgs/applications/science/biology/hisat2/default.nix @@ -42,7 +42,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Graph based aligner"; license = licenses.gpl3; - homepage = https://ccb.jhu.edu/software/hisat2/index.shtml; + homepage = "https://ccb.jhu.edu/software/hisat2/index.shtml"; maintainers = with maintainers; [ jbedo ]; platforms = [ "x86_64-linux" "i686-linux" ]; }; diff --git a/pkgs/applications/science/biology/hmmer/default.nix b/pkgs/applications/science/biology/hmmer/default.nix index 69ecb228697b6..3786b62f7477f 100644 --- a/pkgs/applications/science/biology/hmmer/default.nix +++ b/pkgs/applications/science/biology/hmmer/default.nix @@ -17,7 +17,7 @@ stdenv.mkDerivation rec { HMMER is designed to detect remote homologs as sensitively as possible, relying on the strength of its underlying probability models. In the past, this strength came at significant computational expense, but as of the new HMMER3 project, HMMER is now essentially as fast as BLAST. HMMER can be downloaded and installed as a command line tool on your own hardware, and now it is also more widely accessible to the scientific community via new search servers at the European Bioinformatics Institute. ''; - homepage = http://hmmer.org/; + homepage = "http://hmmer.org/"; license = licenses.gpl3; maintainers = [ maintainers.iimog ]; platforms = [ "x86_64-linux" "i686-linux" ]; diff --git a/pkgs/applications/science/biology/igv/default.nix b/pkgs/applications/science/biology/igv/default.nix index 04699a84b692d..aa6c95071b7bb 100644 --- a/pkgs/applications/science/biology/igv/default.nix +++ b/pkgs/applications/science/biology/igv/default.nix @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { ''; meta = with stdenv.lib; { - homepage = https://www.broadinstitute.org/igv/; + homepage = "https://www.broadinstitute.org/igv/"; description = "A visualization tool for interactive exploration of genomic datasets"; license = licenses.lgpl21; platforms = platforms.unix; diff --git a/pkgs/applications/science/biology/itsx/default.nix b/pkgs/applications/science/biology/itsx/default.nix index 1ba8cdf22ba02..ac534a4ec3cd4 100644 --- a/pkgs/applications/science/biology/itsx/default.nix +++ b/pkgs/applications/science/biology/itsx/default.nix @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing"; - homepage = https://microbiology.se/software/itsx/; + homepage = "https://microbiology.se/software/itsx/"; license = licenses.gpl3; maintainers = [ maintainers.bzizou ]; platforms = [ "x86_64-linux" "i686-linux" ]; diff --git a/pkgs/applications/science/biology/iv/default.nix b/pkgs/applications/science/biology/iv/default.nix index 37abcf396211a..82fe36940081b 100644 --- a/pkgs/applications/science/biology/iv/default.nix +++ b/pkgs/applications/science/biology/iv/default.nix @@ -26,7 +26,7 @@ stdenv.mkDerivation rec meta = with stdenv.lib; { description = "InterViews graphical library for Neuron"; license = licenses.bsd3; - homepage = http://www.neuron.yale.edu/neuron; + homepage = "http://www.neuron.yale.edu/neuron"; platforms = platforms.all; }; } diff --git a/pkgs/applications/science/biology/megahit/default.nix b/pkgs/applications/science/biology/megahit/default.nix index 86414980177f8..35ef280ed676e 100644 --- a/pkgs/applications/science/biology/megahit/default.nix +++ b/pkgs/applications/science/biology/megahit/default.nix @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph"; license = licenses.gpl3; - homepage = https://github.com/voutcn/megahit; + homepage = "https://github.com/voutcn/megahit"; maintainers = with maintainers; [ luispedro ]; platforms = [ "x86_64-linux" ]; }; diff --git a/pkgs/applications/science/biology/messer-slim/default.nix b/pkgs/applications/science/biology/messer-slim/default.nix index d485666f39313..201e38cfc5383 100644 --- a/pkgs/applications/science/biology/messer-slim/default.nix +++ b/pkgs/applications/science/biology/messer-slim/default.nix @@ -18,7 +18,7 @@ stdenv.mkDerivation rec { meta = { description = "An evolutionary simulation framework"; - homepage = https://messerlab.org/slim/; + homepage = "https://messerlab.org/slim/"; license = with stdenv.lib.licenses; [ gpl3 ]; maintainers = with stdenv.lib.maintainers; [ bzizou ]; platforms = stdenv.lib.platforms.all; diff --git a/pkgs/applications/science/biology/migrate/default.nix b/pkgs/applications/science/biology/migrate/default.nix index d80e6e7b30df6..0e2aa1c1a7915 100644 --- a/pkgs/applications/science/biology/migrate/default.nix +++ b/pkgs/applications/science/biology/migrate/default.nix @@ -16,7 +16,7 @@ gccStdenv.mkDerivation rec { meta = with gccStdenv.lib; { description = "Estimates population size, migration, population splitting parameters using genetic/genomic data"; - homepage = https://peterbeerli.com/migrate-html5/index.html; + homepage = "https://peterbeerli.com/migrate-html5/index.html"; license = licenses.mit; maintainers = [ maintainers.bzizou ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/biology/minc-tools/default.nix b/pkgs/applications/science/biology/minc-tools/default.nix index 4c8b768a56a91..db803ea4922f0 100644 --- a/pkgs/applications/science/biology/minc-tools/default.nix +++ b/pkgs/applications/science/biology/minc-tools/default.nix @@ -33,7 +33,7 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; meta = with stdenv.lib; { - homepage = https://github.com/BIC-MNI/minc-tools; + homepage = "https://github.com/BIC-MNI/minc-tools"; description = "Command-line utilities for working with MINC files"; maintainers = with maintainers; [ bcdarwin ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/biology/minimap2/default.nix b/pkgs/applications/science/biology/minimap2/default.nix index bff2bcf428b53..e33a17537910b 100644 --- a/pkgs/applications/science/biology/minimap2/default.nix +++ b/pkgs/applications/science/biology/minimap2/default.nix @@ -22,7 +22,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "A versatile pairwise aligner for genomic and spliced nucleotide sequences"; - homepage = https://lh3.github.io/minimap2; + homepage = "https://lh3.github.io/minimap2"; license = licenses.mit; platforms = platforms.all; maintainers = [ maintainers.arcadio ]; diff --git a/pkgs/applications/science/biology/mni_autoreg/default.nix b/pkgs/applications/science/biology/mni_autoreg/default.nix index ab22fb7232ffb..254d874f9d912 100644 --- a/pkgs/applications/science/biology/mni_autoreg/default.nix +++ b/pkgs/applications/science/biology/mni_autoreg/default.nix @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { ''; meta = with stdenv.lib; { - homepage = https://github.com/BIC-MNI/mni_autoreg; + homepage = "https://github.com/BIC-MNI/mni_autoreg"; description = "Tools for automated registration using the MINC image format"; maintainers = with maintainers; [ bcdarwin ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/biology/mosdepth/default.nix b/pkgs/applications/science/biology/mosdepth/default.nix index 717b8c3ab2f3f..569c63afa7a16 100644 --- a/pkgs/applications/science/biology/mosdepth/default.nix +++ b/pkgs/applications/science/biology/mosdepth/default.nix @@ -38,7 +38,7 @@ in stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing."; license = licenses.mit; - homepage = https://github.com/brentp/mosdepth; + homepage = "https://github.com/brentp/mosdepth"; maintainers = with maintainers; [ jbedo ]; platforms = platforms.linux; }; diff --git a/pkgs/applications/science/biology/mrbayes/default.nix b/pkgs/applications/science/biology/mrbayes/default.nix index 1dd92af58eb1e..8ee7bccf075fe 100644 --- a/pkgs/applications/science/biology/mrbayes/default.nix +++ b/pkgs/applications/science/biology/mrbayes/default.nix @@ -23,7 +23,7 @@ stdenv.mkDerivation rec { MCMC) to approximate the posterior probabilities of trees. ''; license = "GPL2"; - homepage = http://mrbayes.csit.fsu.edu/; + homepage = "http://mrbayes.csit.fsu.edu/"; platforms = stdenv.lib.platforms.linux; }; } diff --git a/pkgs/applications/science/biology/muscle/default.nix b/pkgs/applications/science/biology/muscle/default.nix index 9cbabc7ab37ed..7ed18349259e3 100644 --- a/pkgs/applications/science/biology/muscle/default.nix +++ b/pkgs/applications/science/biology/muscle/default.nix @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "A multiple sequence alignment method with reduced time and space complexity"; license = licenses.publicDomain; - homepage = https://www.drive5.com/muscle/; + homepage = "https://www.drive5.com/muscle/"; maintainers = [ maintainers.unode ]; # NOTE: Supposed to be compatible with darwin/intel & PPC but currently fails. # Anyone with access to these platforms is welcome to give it a try diff --git a/pkgs/applications/science/biology/ncbi-tools/default.nix b/pkgs/applications/science/biology/ncbi-tools/default.nix index 1c24ef0925421..cc8ebf7f37d93 100644 --- a/pkgs/applications/science/biology/ncbi-tools/default.nix +++ b/pkgs/applications/science/biology/ncbi-tools/default.nix @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { meta = { description = ''NCBI Bioinformatics toolbox (incl. BLAST)''; longDescription = ''The NCBI Bioinformatics toolsbox, including command-line utilties, libraries and include files. No X11 support''; - homepage = http://www.ncbi.nlm.nih.gov/IEB/ToolBox/; + homepage = "http://www.ncbi.nlm.nih.gov/IEB/ToolBox/"; license = "GPL"; priority = 5; # zlib.so gives a conflict with zlib broken = true; diff --git a/pkgs/applications/science/biology/neuron/default.nix b/pkgs/applications/science/biology/neuron/default.nix index 4e6d3494c7216..8cad5f466c5f0 100644 --- a/pkgs/applications/science/biology/neuron/default.nix +++ b/pkgs/applications/science/biology/neuron/default.nix @@ -78,7 +78,7 @@ stdenv.mkDerivation rec { involving many ion-specific channels, ion accumulation, and second messengers"; license = licenses.bsd3; - homepage = http://www.neuron.yale.edu/neuron; + homepage = "http://www.neuron.yale.edu/neuron"; maintainers = [ maintainers.adev ]; # source claims it's only tested for x86 and powerpc platforms = platforms.x86_64 ++ platforms.i686; diff --git a/pkgs/applications/science/biology/niftyreg/default.nix b/pkgs/applications/science/biology/niftyreg/default.nix index 48bd1b21ecd6c..fd7dc4f1fbb4f 100644 --- a/pkgs/applications/science/biology/niftyreg/default.nix +++ b/pkgs/applications/science/biology/niftyreg/default.nix @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; meta = with stdenv.lib; { - homepage = http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftyReg; + homepage = "http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftyReg"; description = "Medical image registration software"; maintainers = with maintainers; [ bcdarwin ]; platforms = [ "x86_64-linux" ]; diff --git a/pkgs/applications/science/biology/niftyseg/default.nix b/pkgs/applications/science/biology/niftyseg/default.nix index f70054e97716b..38194697223de 100644 --- a/pkgs/applications/science/biology/niftyseg/default.nix +++ b/pkgs/applications/science/biology/niftyseg/default.nix @@ -13,7 +13,7 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; meta = with stdenv.lib; { - homepage = http://cmictig.cs.ucl.ac.uk/research/software/software-nifty/niftyseg; + homepage = "http://cmictig.cs.ucl.ac.uk/research/software/software-nifty/niftyseg"; description = "Software for medical image segmentation, bias field correction, and cortical thickness calculation"; maintainers = with maintainers; [ bcdarwin ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/biology/paml/default.nix b/pkgs/applications/science/biology/paml/default.nix index 731e31c588fa8..7a2dc2782ab0a 100644 --- a/pkgs/applications/science/biology/paml/default.nix +++ b/pkgs/applications/science/biology/paml/default.nix @@ -28,6 +28,6 @@ stdenv.mkDerivation rec { description = "Phylogenetic Analysis by Maximum Likelihood (PAML)"; longDescription = ''PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.''; license = "non-commercial"; - homepage = http://abacus.gene.ucl.ac.uk/software/paml.html; + homepage = "http://abacus.gene.ucl.ac.uk/software/paml.html"; }; } diff --git a/pkgs/applications/science/biology/platypus/default.nix b/pkgs/applications/science/biology/platypus/default.nix index 6907c6e3ec82e..30e45d5af0ecb 100644 --- a/pkgs/applications/science/biology/platypus/default.nix +++ b/pkgs/applications/science/biology/platypus/default.nix @@ -31,7 +31,7 @@ in stdenv.mkDerivation { meta = with stdenv.lib; { description = "The Platypus variant caller"; license = licenses.gpl3; - homepage = https://github.com/andyrimmer/Platypus; + homepage = "https://github.com/andyrimmer/Platypus"; maintainers = with maintainers; [ jbedo ]; platforms = platforms.x86_64; }; diff --git a/pkgs/applications/science/biology/plink-ng/default.nix b/pkgs/applications/science/biology/plink-ng/default.nix index 52f8f70b7796a..13f00c53fe642 100644 --- a/pkgs/applications/science/biology/plink-ng/default.nix +++ b/pkgs/applications/science/biology/plink-ng/default.nix @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { meta = { description = "A comprehensive update to the PLINK association analysis toolset"; - homepage = https://www.cog-genomics.org/plink2; + homepage = "https://www.cog-genomics.org/plink2"; license = stdenv.lib.licenses.gpl3; platforms = stdenv.lib.platforms.linux; }; diff --git a/pkgs/applications/science/biology/plink/default.nix b/pkgs/applications/science/biology/plink/default.nix index cc48a0cb13a93..009e12aa02f0f 100644 --- a/pkgs/applications/science/biology/plink/default.nix +++ b/pkgs/applications/science/biology/plink/default.nix @@ -17,7 +17,7 @@ stdenv.mkDerivation { meta = { description = "Whole genome association toolkit"; - homepage = http://pngu.mgh.harvard.edu/~purcell/plink/; + homepage = "http://pngu.mgh.harvard.edu/~purcell/plink/"; license = stdenv.lib.licenses.gpl2; platforms = stdenv.lib.platforms.all; broken = true; diff --git a/pkgs/applications/science/biology/poretools/default.nix b/pkgs/applications/science/biology/poretools/default.nix index 4660a776ab219..a9f3fdb246726 100755 --- a/pkgs/applications/science/biology/poretools/default.nix +++ b/pkgs/applications/science/biology/poretools/default.nix @@ -16,7 +16,7 @@ pythonPackages.buildPythonPackage rec { meta = { description = "a toolkit for working with nanopore sequencing data from Oxford Nanopore"; license = stdenv.lib.licenses.mit; - homepage = https://poretools.readthedocs.io/en/latest/; + homepage = "https://poretools.readthedocs.io/en/latest/"; maintainers = [stdenv.lib.maintainers.rybern]; }; } diff --git a/pkgs/applications/science/biology/prodigal/default.nix b/pkgs/applications/science/biology/prodigal/default.nix index 653f4390488e2..ba51c93c38c25 100644 --- a/pkgs/applications/science/biology/prodigal/default.nix +++ b/pkgs/applications/science/biology/prodigal/default.nix @@ -18,7 +18,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Fast, reliable protein-coding gene prediction for prokaryotic genomes"; - homepage = https://github.com/hyattpd/Prodigal; + homepage = "https://github.com/hyattpd/Prodigal"; license = licenses.gpl3; platforms = platforms.all; maintainers = with maintainers; [ luispedro ]; diff --git a/pkgs/applications/science/biology/raxml/default.nix b/pkgs/applications/science/biology/raxml/default.nix index d7ee54bfbcf03..5c7353af9315c 100644 --- a/pkgs/applications/science/biology/raxml/default.nix +++ b/pkgs/applications/science/biology/raxml/default.nix @@ -33,7 +33,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies"; license = licenses.gpl3; - homepage = https://sco.h-its.org/exelixis/web/software/raxml/; + homepage = "https://sco.h-its.org/exelixis/web/software/raxml/"; maintainers = [ maintainers.unode ]; platforms = [ "i686-linux" "x86_64-linux" ]; }; diff --git a/pkgs/applications/science/biology/samtools/default.nix b/pkgs/applications/science/biology/samtools/default.nix index f2c5e9f25beba..e750eea89ac9f 100644 --- a/pkgs/applications/science/biology/samtools/default.nix +++ b/pkgs/applications/science/biology/samtools/default.nix @@ -27,7 +27,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Tools for manipulating SAM/BAM/CRAM format"; license = licenses.mit; - homepage = http://www.htslib.org/; + homepage = "http://www.htslib.org/"; platforms = platforms.unix; maintainers = [ maintainers.mimame ]; }; diff --git a/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix b/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix index 72d125ef8b6f3..d62c2a1fe7b1a 100644 --- a/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix +++ b/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Tools for manipulating SAM/BAM/CRAM format"; license = licenses.mit; - homepage = http://samtools.sourceforge.net/; + homepage = "http://samtools.sourceforge.net/"; platforms = platforms.unix; maintainers = [ maintainers.unode ]; }; diff --git a/pkgs/applications/science/biology/snpeff/default.nix b/pkgs/applications/science/biology/snpeff/default.nix index d700ee50a9c6b..c68fcfada3325 100644 --- a/pkgs/applications/science/biology/snpeff/default.nix +++ b/pkgs/applications/science/biology/snpeff/default.nix @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Genetic variant annotation and effect prediction toolbox."; license = licenses.lgpl3; - homepage = http://snpeff.sourceforge.net/; + homepage = "http://snpeff.sourceforge.net/"; maintainers = with maintainers; [ jbedo ]; platforms = platforms.all; }; diff --git a/pkgs/applications/science/biology/somatic-sniper/default.nix b/pkgs/applications/science/biology/somatic-sniper/default.nix index 1961c71f43bb0..17d9c3dbb55cd 100644 --- a/pkgs/applications/science/biology/somatic-sniper/default.nix +++ b/pkgs/applications/science/biology/somatic-sniper/default.nix @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Identify single nucleotide positions that are different between tumor and normal"; license = licenses.mit; - homepage = https://github.com/genome/somatic-sniper; + homepage = "https://github.com/genome/somatic-sniper"; maintainers = with maintainers; [ jbedo ]; platforms = platforms.linux; }; diff --git a/pkgs/applications/science/biology/sortmerna/default.nix b/pkgs/applications/science/biology/sortmerna/default.nix index 4adce4461ede6..1f291d1a7008d 100644 --- a/pkgs/applications/science/biology/sortmerna/default.nix +++ b/pkgs/applications/science/biology/sortmerna/default.nix @@ -32,7 +32,7 @@ stdenv.mkDerivation rec { description = "Tools for filtering, mapping, and OTU-picking from shotgun genomics data"; license = licenses.lgpl3; platforms = platforms.x86_64; - homepage = https://bioinfo.lifl.fr/RNA/sortmerna/; + homepage = "https://bioinfo.lifl.fr/RNA/sortmerna/"; maintainers = with maintainers; [ luispedro ]; }; } diff --git a/pkgs/applications/science/biology/strelka/default.nix b/pkgs/applications/science/biology/strelka/default.nix index 184dcb48a0de0..a32eddcb1cd93 100644 --- a/pkgs/applications/science/biology/strelka/default.nix +++ b/pkgs/applications/science/biology/strelka/default.nix @@ -35,7 +35,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Germline and small variant caller"; license = licenses.gpl3; - homepage = https://github.com/Illumina/strelka; + homepage = "https://github.com/Illumina/strelka"; maintainers = with maintainers; [ jbedo ]; platforms = [ "x86_64-linux" ]; }; diff --git a/pkgs/applications/science/biology/sumatools/default.nix b/pkgs/applications/science/biology/sumatools/default.nix index 5230fcd2eb62f..1e3b479d54fc7 100644 --- a/pkgs/applications/science/biology/sumatools/default.nix +++ b/pkgs/applications/science/biology/sumatools/default.nix @@ -4,7 +4,7 @@ let stdenv = gccStdenv; meta = with stdenv.lib; { description = "Fast and exact comparison and clustering of sequences"; - homepage = https://metabarcoding.org/sumatra; + homepage = "https://metabarcoding.org/sumatra"; maintainers = [ maintainers.bzizou ]; platforms = platforms.unix; }; diff --git a/pkgs/applications/science/biology/trimal/default.nix b/pkgs/applications/science/biology/trimal/default.nix index d4e8fee7bc364..8d7e62b614316 100755 --- a/pkgs/applications/science/biology/trimal/default.nix +++ b/pkgs/applications/science/biology/trimal/default.nix @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { description = "A tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment"; license = licenses.gpl3; platforms = platforms.linux; - homepage = http://trimal.cgenomics.org; + homepage = "http://trimal.cgenomics.org"; maintainers = [ maintainers.bzizou ]; }; } diff --git a/pkgs/applications/science/biology/varscan/default.nix b/pkgs/applications/science/biology/varscan/default.nix index 697a444193b11..e97c8f14451f7 100644 --- a/pkgs/applications/science/biology/varscan/default.nix +++ b/pkgs/applications/science/biology/varscan/default.nix @@ -28,7 +28,7 @@ stdenv.mkDerivation rec { # through the Office of Technology Management at Washington # University School of Medicine. license = licenses.unfree; - homepage = https://github.com/dkoboldt/varscan; + homepage = "https://github.com/dkoboldt/varscan"; maintainers = with maintainers; [ jbedo ]; platforms = platforms.all; }; diff --git a/pkgs/applications/science/biology/vcftools/default.nix b/pkgs/applications/science/biology/vcftools/default.nix index f6c9ad029c135..52957b58bc929 100755 --- a/pkgs/applications/science/biology/vcftools/default.nix +++ b/pkgs/applications/science/biology/vcftools/default.nix @@ -17,7 +17,7 @@ stdenv.mkDerivation rec { description = "A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project"; license = licenses.lgpl3; platforms = platforms.linux; - homepage = https://vcftools.github.io/index.html; + homepage = "https://vcftools.github.io/index.html"; maintainers = [ maintainers.rybern ]; }; } |