biology/igv 2.19.8
Visualization tool for genomic datasets
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
a4679caacd- License
- MIT
- Categories
- biology, java
- Package size
- 31330.9 KiB, 62299.9 KiB installed
Description
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
Install
As a binary package — by origin, or by package name:
pkg install biology/igv
pkg install igvFrom the ports tree:
cd /usr/ports/biology/igv/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= igv>0:biology/igvPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 2.16.0_3 | 2.16.0_3 | - | - | - |
| FreeBSD:14:quarterly | 2.16.0_3 | 2.16.0_3 | n/a | - | 2.16.0_3 |
| FreeBSD:15:latest | 2.16.0_3 | 2.16.0_3 | n/a | - | 2.16.0_1 |
| FreeBSD:15:quarterly | 2.16.0_3 | 2.16.0_3 | n/a | n/a | n/a |
| FreeBSD:16:latest | 2.16.0_3 | - | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Build 1
gradle8: devel/gradle8
The full lists below include those, and their dependencies in turn.
All build dependencies 54
- archivers/brotli
- archivers/libdeflate
- archivers/liblz4
- archivers/zstd
- audio/alsa-lib
- converters/libiconv
- devel/gettext-runtime
- devel/glib20
- devel/gradle8
- devel/libffi
- devel/libinotify
- devel/pcre2
- devel/py-packaging
- devel/readline
- graphics/giflib
- graphics/graphite2
- graphics/jbigkit
- graphics/jpeg-turbo
- graphics/lcms2
- graphics/lerc
- graphics/png
- graphics/tiff
- java/javavmwrapper
- java/openjdk21
- lang/python312
- lang/python315
- math/mpdecimal
- print/freetype2
- print/harfbuzz
- print/indexinfo
- textproc/expat2
- x11-fonts/dejavu
- x11-fonts/encodings
- x11-fonts/font-bh-ttf
- x11-fonts/font-misc-ethiopic
- x11-fonts/font-misc-meltho
- x11-fonts/fontconfig
- x11-fonts/libfontenc
- x11-fonts/mkfontscale
- x11-fonts/xorg-fonts-truetype
- x11-toolkits/libXt
- x11/libICE
- x11/libSM
- x11/libX11
- x11/libXau
- x11/libXdmcp
- x11/libXext
- x11/libXfixes
- x11/libXi
- x11/libXrandr
- x11/libXrender
- x11/libXtst
- x11/libxcb
- x11/xorgproto
All run dependencies 53
- archivers/brotli
- archivers/libdeflate
- archivers/liblz4
- archivers/zstd
- audio/alsa-lib
- converters/libiconv
- devel/gettext-runtime
- devel/glib20
- devel/libffi
- devel/libinotify
- devel/pcre2
- devel/py-packaging
- devel/readline
- graphics/giflib
- graphics/graphite2
- graphics/jbigkit
- graphics/jpeg-turbo
- graphics/lcms2
- graphics/lerc
- graphics/png
- graphics/tiff
- java/javavmwrapper
- java/openjdk21
- lang/python312
- lang/python315
- math/mpdecimal
- print/freetype2
- print/harfbuzz
- print/indexinfo
- textproc/expat2
- x11-fonts/dejavu
- x11-fonts/encodings
- x11-fonts/font-bh-ttf
- x11-fonts/font-misc-ethiopic
- x11-fonts/font-misc-meltho
- x11-fonts/fontconfig
- x11-fonts/libfontenc
- x11-fonts/mkfontscale
- x11-fonts/xorg-fonts-truetype
- x11-toolkits/libXt
- x11/libICE
- x11/libSM
- x11/libX11
- x11/libXau
- x11/libXdmcp
- x11/libXext
- x11/libXfixes
- x11/libXi
- x11/libXrandr
- x11/libXrender
- x11/libXtst
- x11/libxcb
- x11/xorgproto
Required by 1
Configuration
No options to configure.
- USES
- gettext-runtime java
- Service scripts
- none
Files
pkg-plist 290
- bin/igv
- %%JAVAJARDIR%%/igv/AbsoluteLayout-RELEASE110-module.jar
- %%JAVAJARDIR%%/igv/annotations-2.30.17.jar
- %%JAVAJARDIR%%/igv/apache-client-2.30.17.jar
- %%JAVAJARDIR%%/igv/arns-2.30.17.jar
- %%JAVAJARDIR%%/igv/asm-7.3.1.jar
- %%JAVAJARDIR%%/igv/asm-analysis-7.3.1.jar
- %%JAVAJARDIR%%/igv/asm-commons-7.3.1.jar
- %%JAVAJARDIR%%/igv/asm-tree-7.3.1.jar
- %%JAVAJARDIR%%/igv/asm-util-7.3.1.jar
- %%JAVAJARDIR%%/igv/auth-2.30.17.jar
- %%JAVAJARDIR%%/igv/aws-core-2.30.17.jar
- %%JAVAJARDIR%%/igv/aws-json-protocol-2.30.17.jar
- %%JAVAJARDIR%%/igv/aws-query-protocol-2.30.17.jar
- %%JAVAJARDIR%%/igv/aws-xml-protocol-2.30.17.jar
- %%JAVAJARDIR%%/igv/batik-awt-util-1.17-module.jar
- %%JAVAJARDIR%%/igv/batik-codec-1.17-module.jar
- %%JAVAJARDIR%%/igv/batik-constants-1.17-module.jar
- %%JAVAJARDIR%%/igv/batik-dom-1.17-module.jar
- %%JAVAJARDIR%%/igv/batik-ext-1.17-module.jar
- %%JAVAJARDIR%%/igv/batik-i18n-1.17-module.jar
- %%JAVAJARDIR%%/igv/batik-shared-resources-1.17-module.jar
- %%JAVAJARDIR%%/igv/batik-svggen-1.17-module.jar
- %%JAVAJARDIR%%/igv/batik-transcoder-1.17-module.jar
- %%JAVAJARDIR%%/igv/batik-util-1.17-module.jar
- %%JAVAJARDIR%%/igv/batik-xml-1.17-module.jar
- %%JAVAJARDIR%%/igv/checksums-2.30.17.jar
- %%JAVAJARDIR%%/igv/checksums-spi-2.30.17.jar
- %%JAVAJARDIR%%/igv/cognitoidentity-2.30.17.jar
- %%JAVAJARDIR%%/igv/commons-codec-1.17.1.jar
- %%JAVAJARDIR%%/igv/commons-compress-1.26.0.jar
- %%JAVAJARDIR%%/igv/commons-io-2.15.1.jar
- %%JAVAJARDIR%%/igv/commons-jexl-2.1.1-module.jar
- %%JAVAJARDIR%%/igv/commons-lang3-3.14.0.jar
- %%JAVAJARDIR%%/igv/commons-logging-1.3.0.jar
- %%JAVAJARDIR%%/igv/commons-math3-3.6.1-module.jar
- %%JAVAJARDIR%%/igv/crt-core-2.30.17.jar
- %%JAVAJARDIR%%/igv/endpoints-spi-2.30.17.jar
- %%JAVAJARDIR%%/igv/eventstream-1.0.1.jar
- %%JAVAJARDIR%%/igv/genomes/129S1_SvImJ.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/1kg_ref.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/1kg_v37.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/1kg_v37_alias.tab
- %%JAVAJARDIR%%/igv/genomes/2019-03-21_Creinhardtii_CC-503_v5.5.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/2019-03-21_Creinhardtii_CC-503_v5.6.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/2019-03-21_Creinhardtii_CC-503_v5.6_Cp+Mt_v4.4.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/ABaumannii_ATCC_17978.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/ABaumannii_AYE_uid61637.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/AGPv3.31.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/ASM294v2.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/ASM985889v3.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/AgamP3.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/Aplysia.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/B73.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/CCAF000000000.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/CE_1.0.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/CSavignyi_v2.1.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/D.discoideum.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/EBV_Type2.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/Foxy4287.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/GCF_000233375.1.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/GCF_000364345.1.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/GCF_016920785.1.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/GSM552910.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/GSM552910_alias.tab
- %%JAVAJARDIR%%/igv/genomes/Glamblia_2.0.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/HHV4_Type1.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/ITAG2.3.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/ITAG2.3_alias.tab
- %%JAVAJARDIR%%/igv/genomes/M74568.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/MusPutFur1.0.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/MusaAcuminata.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/MusaBalbisianaPKWv1.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/NC_000913.2.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/NC_000913.2_alias.tab
- %%JAVAJARDIR%%/igv/genomes/NC_000913.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/NC_000964.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/NC_001405.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/NC_001422.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/NC_001623.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/NC_001722.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/NC_001802.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/NC_002655.2.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/NC_002755.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/NC_002929.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/NC_003112.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/NC_003116.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/NC_004917.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/NC_008601.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/NC_008767.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/NC_009012.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/NC_009012_alias.tab
- %%JAVAJARDIR%%/igv/genomes/NC_012920.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/NC_016856.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/O_Sativa_r6.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/OryCun2.0.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/Pf3D7_v9.0.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/Pf3D7_v9.0_alias.tab
- %%JAVAJARDIR%%/igv/genomes/PlasmoDB_24.chrom.sizes
- %%JAVAJARDIR%%/igv/genomes/PlasmoDB_7.0.chrom.sizes
The first 100 are listed.
distinfo 3
| File | Size | SHA256 |
|---|---|---|
| igv-2.19.8/tools.png | 17414 | d2721646a4bb9ef248da85639e11eb7bbcf2685396f9b6f8a325b77b127fac4e |
| igv-2.19.8/igv-2.19.8-deps.tar.gz | 4.9531238e+07 | cc44c8159e866523634af1eea6a5d5a02acbc2a316fbc61cd1a6090f840607f1 |
| igv-2.19.8/igvteam-igv-v2.19.8_GH0.tar.gz | 6.495357e+07 | 9845c299996ae8196c71688fe3f950ad5953f80aa952fdeb736009d7c71208be |
Master sites 1
- http://software.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/:img