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Port details
pear-merger Memory-efficient and highly accurate paired-end read merger
0.9.6_1 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.9.6Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-04 17:21:55
Last Update: 2024-01-12 15:11:29
Commit Hash: d432922
License: CC-BY-NC-SA-3.0
WWW:
https://sco.h-its.org/exelixis/web/software/pear/
Description:
PEAR is an ultrafast, memory-efficient and highly accurate paired-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (5 items)
Collapse this list.
  1. bin/pearRM
  2. share/man/man1/pearRM.1.gz
  3. /usr/local/share/licenses/pear-merger-0.9.6_1/catalog.mk
  4. /usr/local/share/licenses/pear-merger-0.9.6_1/LICENSE
  5. /usr/local/share/licenses/pear-merger-0.9.6_1/CC-BY-NC-SA-3.0
Collapse this list.
Dependency lines:
  • pear-merger>0:biology/pear-merger
To install the port:
cd /usr/ports/biology/pear-merger/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/pear-merger
  • pkg install pear-merger
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: pear-merger
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1519766031 SHA256 (pear_0.9.6_src_all.tar.gz) = f7728371e26a5b46fa928b0f7ae1b552ed6a78815b117ba48ef1af98e96c8e2b SIZE (pear_0.9.6_src_all.tar.gz) = 292790

Packages (timestamps in pop-ups are UTC):
pear-merger
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest0.9.6_10.9.6_1-0.9.6_10.9.6_1---
FreeBSD:13:quarterly0.9.60.9.6-0.9.60.9.6-0.9.60.9.6
FreeBSD:14:latest0.9.6_10.9.6_1-0.9.6_10.9.6_1---
FreeBSD:14:quarterly0.9.60.9.6-0.9.60.9.6-0.9.60.9.6
FreeBSD:15:latest0.9.6_10.9.6_1n/a0.9.6_1n/a-0.9.6_10.9.6_1
FreeBSD:15:quarterly--n/a-n/a---
This port has no dependencies.
This port is required by:
for Run
  1. biology/ddocent

Configuration Options:
No options to configure
Options name:
biology_pear-merger
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://depot.galaxyproject.org/software/pear/
Collapse this list.

Number of commits found: 10

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.9.6_1
12 Jan 2024 15:11:29
commit hash: d4329229fbe8ad0a96a1b9ec796d17cf512455d1commit hash: d4329229fbe8ad0a96a1b9ec796d17cf512455d1commit hash: d4329229fbe8ad0a96a1b9ec796d17cf512455d1commit hash: d4329229fbe8ad0a96a1b9ec796d17cf512455d1 files touched by this commit
Baptiste Daroussin (bapt) search for other commits by this committer
MANPREFIX: eliminate its usage

While here move manpages to share/man
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
0.9.6
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
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.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.9.6
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
0.9.6
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
0.9.6
06 Apr 2021 13:04:16
commit hash: 8f0ebbe09b53d252688d90d716bd46db3df6d47bcommit hash: 8f0ebbe09b53d252688d90d716bd46db3df6d47bcommit hash: 8f0ebbe09b53d252688d90d716bd46db3df6d47bcommit hash: 8f0ebbe09b53d252688d90d716bd46db3df6d47b files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/pear-merger: enable on aarch64, armv6, armv7, riscv64

It should build now.
0.9.6
06 Apr 2021 09:50:56
commit hash: 2ffa084df93c5ae30d1ce0a9fba1f4f0c902212ecommit hash: 2ffa084df93c5ae30d1ce0a9fba1f4f0c902212ecommit hash: 2ffa084df93c5ae30d1ce0a9fba1f4f0c902212ecommit hash: 2ffa084df93c5ae30d1ce0a9fba1f4f0c902212e files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/pear-merger: fix build on non-x86

Builds fine with GCC.
0.9.6
02 Jan 2021 01:46:09
Revision:559904Original commit files touched by this commit
linimon search for other commits by this committer
For ports on riscv64 that fail the same (or similar ways) to aarch64, mark
them BROKEN.

While here, pet portlint (Makevar order).

Approved by:	portmgr (tier-2 blanket)
0.9.6
21 Jun 2018 23:52:37
Revision:473009Original commit files touched by this commit
linimon search for other commits by this committer
Mark as broken on aarch64, and, where appropriate, armvX.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
0.9.6
04 Apr 2018 17:21:39
Revision:466449Original commit files touched by this commit
jwb search for other commits by this committer
biology/pear-merger: Memory-efficient and accurate paired-end read merger

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D14959

Number of commits found: 10