biology/sra-tools3.4.1_3

Release numerous ports to ports@

I've been retired for a few years, and it is unlikely I will be doing
any more scientific computing support in the future.  I have continued
to maintain ~160 ports to the best of my ability, mainly as a favor to
the community, but I can no longer justify the time and effort
required.  I am therefore releasing most of my scientific ports, along
with a few others, to ports@.  I will continue to maintain ports I am
actively using and those for which I am upstream.

biology/sra-tools: lib64 -> lib

Patch to better respect filesystem hierarchy.  The lib64 default was
left alone originally because the old esoteric build system was
difficult to patch.  The new system is much simpler.  Reporter
indicated that the presence of ${PREFIX}/lib64 causes build failures
in some other ports.

PR:             294837
Reported by:    milios@ccsys.com

biology/sra-tools: Patch out extraneous scripts

Build from source was installing scripts directly into /etc/profile.d
that are not even needed when installing from ports.
Also patched out some pip commands to silence poudriere warnings.

PR:             294837
Reported by:    milios@ccsys.com

*/*: bump portrevision after java_default=25 update

Included all ports that have USES=java.

PR:	293559

biology/sra-tools: Unbreak distfile

Corruption caused by failed fetch during previous commit.

biology/sra-tools: Update to 3.4.1

Several minor enhancements and fixes
Changes:
    https://github.com/ncbi/sra-tools/blob/master/CHANGES.md
    https://github.com/ncbi/sra-tools/commits/master/

Reported by:    portscout

*/*: bump portrevision after java_default=21 update

PR:	272855

biology/sra-tools: Unbreak with extra JDK present

Cmake find_package(Java) uses the latest version found, and plist
varies depending on the version used.  Set JAVE_HOME to limit
cmake's search to the version specified in the port.  This is the
only way to control find_package() for Java versions.

biology/sra-tools: pin to java 17

As soon as another JDK is installed it fails the build.
This commit will make it possible to bump JAVA_DEFAULT to 21
while the maintainer looks for a solution to build this port
with other JDK versions.

PR:	292215

biology/sra-tools: Update to 3.3.0

Several minor enhancements and fixes
Changes:
    ${WRKSRC}/CHANGES.md
    https://github.com/ncbi/sra-tools/commits/master/

Reported by:    portscout

biology/sra-tools: Update to 3.2.1

Fix fasterq-dump mkdir error:
https://github.com/ncbi/sra-tools/issues/1016#issuecomment-2737694569
Numerous other fixes and enhancements
Changes: https://github.com/ncbi/sra-tools/commits/master/

Reported by:    portscout

biology/sra-tools: Update to 3.2.0

Numerous fixes and enhancements
Changes: https://github.com/ncbi/sra-tools/commits/master/

Reported by:    portscout

Mk/**java.mk: Convert bsd.java.mk to USES

The following features have been added or changed:
- Instead of USE_JAVA use USES=java. This defaults to
  USES=java:build,run if NO_BUILD is undefined. Else it defaults to
  USES=java:run
- Instead of USE_ANT=yes use USES=java:ant which also implies
  USES=java:build
- Instead of JAVA_BUILD=yes use USES=java:build. Does not imply run or
  extract
- Instead of JAVA_EXTRACT=yes use USES=java:extract does not imply
  build or run
- Instead of JAVA_RUN=yes use USES=java:run does not imply extract or
  build
- Instead of USE_JAVA=<version> use USES=java and JAVA_VERSION=<version>

Approved by: mat (portmgr), glewis
Differential Revision:  https://reviews.freebsd.org/D48201

biology/sra-tools: Update to 3.1.1

Numerous fixes and enhancements since 3.0.6
Changes: https://github.com/ncbi/sra-tools/commits/master/

All previous patches upstreamed
Rewrote pkg-descr to be more introductory

biology/sra-tools: Quick fix to unbreak build

jquery version in pkg-plist changed, not sure why
Port is due for upgrade anyway

cleanup: remove occurrences of WITH_DEBUG

DEBUG like all ports features, must not ever be set in a port, they are
user facing features, that the user needs to enable in their
environment/make.conf, either by defining WITH_DEBUG globally, or by
setting WITH_DEBUG_PORTS with origin of ports they want DEBUG enabled
in.

biology/sra-tools: Update to 3.0.6

Major code and build system rework since 2.11
Now supports aarch64, unblocking rna-seq and atac-seq metaports
Changes: https://github.com/ncbi/sra-tools/commits/master

Reported by:    portscout

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

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)

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)

science/hdf5: bump PORTREVISION of consumers

The SO-version increased in the update to 1.12.2 in
a43418b81530f7e897abfbe18dd59f44265a1a0f .

Reported by:	VVD <vvd@unislabs.com>

biology/sra-tools: Fix build with HDF5 1.12.0+

textproc/libxml2: bump all LIB_DEPENDS consumers

This is a separate commit to facilitate easier cherry-picking for
quarterly.

PR: 262853, 262940, 262877, 263126
Approved by: fluffy (mentor)

textproc/libxml2: bump all dependencies

This should make sure that all dependent ports will pick
up the new version commited with a13ec21cd733f67a9fc0dc00ab45268bdc236246

Fix CONFLICTS entries of multiple ports

There have been lots of missing CONFLICTS_INSTALL entries, either
because conflicting ports were added without updating existing ports,
due to name changes of generated packages, due to mis-understanding
the format and semantics of the conflicts entries, or just due to
typoes in package names.

This patch is the result of a comparison of all files contained in
the official packages with each other. This comparison was based on
packages built with default options and may therefore have missed
further conflicts with optionally installed files.

Where possible, version numbers in conflicts entries have been
generalized, some times taking advantage of the fact that a port
cannot conflict with itself (due to logic in bsd.port.mk that
supresses the pattern match result in that case).

A few ports that set the conflicts variables depending on complex
conditions (e.g. port options), have been left unmodified, despite
probably containing outdated package names.

These changes should only affect the installation of locally built
ports, not the package building with poudriere. They should give an
early indication of the install conflict in cases where currently
the pkg command aborts an installation when it detects that an
existing file would be overwritten,

Approved by:	portmgr (implicit)

biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read Archives

SRA tools is a toolkit for using data in the INSDC Sequence Read Archives.

SRAs operated by International Nucleotide Sequence Database Collaboration
houses sequence reads and alignments generated by "next-gen" sequencers.

This port is a bit convoluted due to the fact that the sra-tools build
requires access to the ncbi-vdb source tree.  Hence, ncbi-vdb is treated
as a submodule here rather than a separate library port.  We are working
with upstream with hope for long-term improvements.