[ 21:53 Jason W. Bacon (jwb)  ]

• d94f19ab9ffcd2fac7650802d6aea3f68156f5d7 biology/ucsc-userapps/Makefile
• d94f19ab9ffcd2fac7650802d6aea3f68156f5d7 biology/ucsc-userapps/files/kent.c
• d94f19ab9ffcd2fac7650802d6aea3f68156f5d7 biology/ucsc-userapps/pkg-plist

biology/ucsc-userapps: Add "kent" command in ${PREFIX}/bin

Standard kent userapps commands are installed under ${PREFIX}/userapps
because of multiple conflicts.  The kent command turns the standard
commands into subcommands, so no special PATH is needed.

    /usr/local/ucsc-userapps/bin/bigWigToBedGraph [args]

can be run as

    kent bigWigToBedGraph [args]

[ 15:23 Jason W. Bacon (jwb)  ]

• 43397d188c684b83c4bff3e9b78862a1f6ab47f7 biology/ucsc-userapps/Makefile
• 43397d188c684b83c4bff3e9b78862a1f6ab47f7 biology/ucsc-userapps/distinfo
• 43397d188c684b83c4bff3e9b78862a1f6ab47f7 biology/ucsc-userapps/pkg-plist

biology/ucsc-userapps: Update to v414

Update license message.  Confirmed via conversation with UCSC that some
proprietary code is used in the "free" tools build.  UCSC is working on it.

[ 17:18 Jason W. Bacon (jwb)  ]

• 6b63ef7436c4e0ec7693779240f1c90fa6e57a57 biology/ucsc-userapps/Makefile
• 6b63ef7436c4e0ec7693779240f1c90fa6e57a57 biology/ucsc-userapps/distinfo
• 6b63ef7436c4e0ec7693779240f1c90fa6e57a57 biology/ucsc-userapps/files/patch-kent_src_hg_encode3_eap_eapFinish_eapFinish.c
• 6b63ef7436c4e0ec7693779240f1c90fa6e57a57 biology/ucsc-userapps/files/patch-kent_src_hg_encode3_encodeDataWarehouse_edwWebRegisterScript_edwWebRegisterScript.c
• 6b63ef7436c4e0ec7693779240f1c90fa6e57a57 biology/ucsc-userapps/files/patch-kent_src_inc_common.mk
• 6b63ef7436c4e0ec7693779240f1c90fa6e57a57 biology/ucsc-userapps/files/patch-kent_src_inc_uuid.h
• 6b63ef7436c4e0ec7693779240f1c90fa6e57a57 biology/ucsc-userapps/files/patch-kent_src_lib_uuid.c
• 6b63ef7436c4e0ec7693779240f1c90fa6e57a57 biology/ucsc-userapps/files/patch-kent_src_utils_dnsInfo_dnsInfo.c
• 6b63ef7436c4e0ec7693779240f1c90fa6e57a57 biology/ucsc-userapps/files/patch-kent_src_utils_dnsInfo_makefile
• 6b63ef7436c4e0ec7693779240f1c90fa6e57a57 biology/ucsc-userapps/files/ucsc-shell.in

biology/ucsc-userapps: Command line tools from the UCSC Genome Browser project

These are the command-line bioinformatics utilities associated with the UCSC
genome browser.  Care has been taken to install only the freely available
tools.  However, the license information at https://genome.ucsc.edu/license/
is not entirely clear and we may add non-free utilities in the future.

Contact UCSC if you are using this port for commercial purposes.