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non port: biology/biostar-tools/Makefile

Number of commits found: 19

Friday, 16 Feb 2024
13:42 Jason W. Bacon (jwb) search for other commits by this committer
biology/biostar-tools: Update to 1.10.1_3

Add sra-tools to metaport deps on aarch64
Clean up pkg-desc
commit hash: 306ace396259a771b353a17bffd1e8465c2ac89d commit hash: 306ace396259a771b353a17bffd1e8465c2ac89d commit hash: 306ace396259a771b353a17bffd1e8465c2ac89d commit hash: 306ace396259a771b353a17bffd1e8465c2ac89d 306ace3
Tuesday, 25 Apr 2023
15:17 Christian Weisgerber (naddy) search for other commits by this committer
audio/opus: bump consumers after update to 1.4
commit hash: feb1fa34f58ea796656b86a81c2a2996b0b03c96 commit hash: feb1fa34f58ea796656b86a81c2a2996b0b03c96 commit hash: feb1fa34f58ea796656b86a81c2a2996b0b03c96 commit hash: feb1fa34f58ea796656b86a81c2a2996b0b03c96 feb1fa3
Sunday, 23 Apr 2023
09:09 Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b 8d3e020
Wednesday, 7 Sep 2022
21:10 Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.

This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.

There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.

The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.

Approved by:		portmgr (tcberner)
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 b7f0544
Wednesday, 1 Dec 2021
15:49 Jason W. Bacon (jwb) search for other commits by this committer
biology/biostar-tools: Allow package build on non-amd64 systems

Only sra-tools is still non-portable, but it will take some time to
add support for other architectures.  In the meantime, allow aarch64
and powerpc64 users to have a biostar-tools package.
commit hash: 70e9e19c3cb7a11ccfef63c91beaf291ea2fb366 commit hash: 70e9e19c3cb7a11ccfef63c91beaf291ea2fb366 commit hash: 70e9e19c3cb7a11ccfef63c91beaf291ea2fb366 commit hash: 70e9e19c3cb7a11ccfef63c91beaf291ea2fb366 70e9e19
Wednesday, 10 Nov 2021
20:52 Jason W. Bacon (jwb) search for other commits by this committer
biostar-tools: Add gffread to metaport deps
commit hash: 17f3e2cbe6f16082e91366537d29d3d53076e295 commit hash: 17f3e2cbe6f16082e91366537d29d3d53076e295 commit hash: 17f3e2cbe6f16082e91366537d29d3d53076e295 commit hash: 17f3e2cbe6f16082e91366537d29d3d53076e295 17f3e2c
Saturday, 30 Oct 2021
15:27 Jason W. Bacon (jwb) search for other commits by this committer
biology/biostar-tools: Add biology/igv to metaport deps
commit hash: 4df7493e10049abc7538f1f5ab1e69f61136a21d commit hash: 4df7493e10049abc7538f1f5ab1e69f61136a21d commit hash: 4df7493e10049abc7538f1f5ab1e69f61136a21d commit hash: 4df7493e10049abc7538f1f5ab1e69f61136a21d 4df7493e
Thursday, 14 Oct 2021
11:53 Jason W. Bacon (jwb) search for other commits by this committer
biology/biostar-tools: Add py-deeptools to metaport deps
commit hash: 9d1d409f4253410995aba30263251bb1e44f62dc commit hash: 9d1d409f4253410995aba30263251bb1e44f62dc commit hash: 9d1d409f4253410995aba30263251bb1e44f62dc commit hash: 9d1d409f4253410995aba30263251bb1e44f62dc 9d1d409
Tuesday, 12 Oct 2021
16:43 Jason W. Bacon (jwb) search for other commits by this committer
biology/biostar-tools: Add biology/bamutil to metaport deps
commit hash: 2e8996e43d715a60fb52850286a25796fc0b9b4c commit hash: 2e8996e43d715a60fb52850286a25796fc0b9b4c commit hash: 2e8996e43d715a60fb52850286a25796fc0b9b4c commit hash: 2e8996e43d715a60fb52850286a25796fc0b9b4c 2e8996e
Monday, 27 Sep 2021
12:14 Jason W. Bacon (jwb) search for other commits by this committer
biology/biostar-tools: Add biology/kallisto run depend to metaport

Also clean up other deps for consistency
commit hash: 96d32d811873af3c99e0e6380de7f6dba3603399 commit hash: 96d32d811873af3c99e0e6380de7f6dba3603399 commit hash: 96d32d811873af3c99e0e6380de7f6dba3603399 commit hash: 96d32d811873af3c99e0e6380de7f6dba3603399 96d32d8
Tuesday, 7 Sep 2021
20:41 Jason W. Bacon (jwb) search for other commits by this committer
biology/biostar-tools: Add biology/sam2pairwise to run deps

Displays pairwise alignments in a SAM file
commit hash: c73e3a89ec729d2d53d2b124839f39497d4d1b69 commit hash: c73e3a89ec729d2d53d2b124839f39497d4d1b69 commit hash: c73e3a89ec729d2d53d2b124839f39497d4d1b69 commit hash: c73e3a89ec729d2d53d2b124839f39497d4d1b69 c73e3a8
Monday, 6 Sep 2021
14:27 Jason W. Bacon (jwb) search for other commits by this committer
biology/biostar-tools: Add mafft, clustal-omega, pywgsim deps

Short-read alignment related tools
commit hash: 0ec8be4158cacaa92d45914082789d936e8e678b commit hash: 0ec8be4158cacaa92d45914082789d936e8e678b commit hash: 0ec8be4158cacaa92d45914082789d936e8e678b commit hash: 0ec8be4158cacaa92d45914082789d936e8e678b 0ec8be4
Tuesday, 24 Aug 2021
16:46 Jason W. Bacon (jwb) search for other commits by this committer
biostar-tools: Update to 1.4.0

Add multiqc, flash, bfc, and jellyfish to metaport deps
commit hash: 1e0d8ce2079e3b116932d1450f249092abc40a3a commit hash: 1e0d8ce2079e3b116932d1450f249092abc40a3a commit hash: 1e0d8ce2079e3b116932d1450f249092abc40a3a commit hash: 1e0d8ce2079e3b116932d1450f249092abc40a3a 1e0d8ce
Friday, 13 Aug 2021
14:16 Jason W. Bacon (jwb) search for other commits by this committer
biostar-tools: Correct category for py-ont-fast5-api
commit hash: 361278dd7c6792f2ef8cb628d385dc8ea287076a commit hash: 361278dd7c6792f2ef8cb628d385dc8ea287076a commit hash: 361278dd7c6792f2ef8cb628d385dc8ea287076a commit hash: 361278dd7c6792f2ef8cb628d385dc8ea287076a 361278d
13:37 Jason W. Bacon (jwb) search for other commits by this committer
biostar-tools: Add new deps to metaport

csvkit, miller: Tools for working with comma-separated data
py-ont-fast5-api: Library and tools for Oxford Nanopore fast5 files
commit hash: 3ed2dd540f07e1493b6f3532f65ae3548b9ad8cb commit hash: 3ed2dd540f07e1493b6f3532f65ae3548b9ad8cb commit hash: 3ed2dd540f07e1493b6f3532f65ae3548b9ad8cb commit hash: 3ed2dd540f07e1493b6f3532f65ae3548b9ad8cb 3ed2dd5
Friday, 9 Jul 2021
12:35 Jason W. Bacon (jwb) search for other commits by this committer
biology/biostar-tools: Add erminej run depend to metaport
commit hash: abcde308144327fccd7d6f6ad0b6f70448b0f275 commit hash: abcde308144327fccd7d6f6ad0b6f70448b0f275 commit hash: abcde308144327fccd7d6f6ad0b6f70448b0f275 commit hash: abcde308144327fccd7d6f6ad0b6f70448b0f275 abcde30
Friday, 2 Jul 2021
17:03 Jason W. Bacon (jwb) search for other commits by this committer
biology/biostar-tools: Add biology/py-goatools to metaport depends
commit hash: 8b48d38ecee37869f24ce0cb1c7ec43037d9d479 commit hash: 8b48d38ecee37869f24ce0cb1c7ec43037d9d479 commit hash: 8b48d38ecee37869f24ce0cb1c7ec43037d9d479 commit hash: 8b48d38ecee37869f24ce0cb1c7ec43037d9d479 8b48d38
Tuesday, 22 Jun 2021
18:00 Jason W. Bacon (jwb) search for other commits by this committer
biostar-tools: Add sra-tools dependency to metaport
commit hash: 1885ed0eb12466cc4aa8ced3c0f8645f4f8a1cf6 commit hash: 1885ed0eb12466cc4aa8ced3c0f8645f4f8a1cf6 commit hash: 1885ed0eb12466cc4aa8ced3c0f8645f4f8a1cf6 commit hash: 1885ed0eb12466cc4aa8ced3c0f8645f4f8a1cf6 1885ed0
Friday, 18 Jun 2021
21:56 Jason W. Bacon (jwb) search for other commits by this committer
biology/biostar-tools: Meta-port for Biostar Handbook tools

Biostar-Tools is a metaport for installing all the tools necessary to work
through the Biostar Handbook, except for bedGrapToBigWig, which has license
restrictions.  If you need bedGraphToBigWig, run

    cd /usr/ports/biology/ucsc-userapps && make install clean
commit hash: 6df92a09ad7a75d3533ac3510cba668c74689255 commit hash: 6df92a09ad7a75d3533ac3510cba668c74689255 commit hash: 6df92a09ad7a75d3533ac3510cba668c74689255 commit hash: 6df92a09ad7a75d3533ac3510cba668c74689255 6df92a0

Number of commits found: 19