[new port] biology/fastqc: Quality control tool for high throughput sequence data

[jwb]

Summary

[new port] biology/fastqc: Quality control tool for high throughput sequence data
Approved by: jrm (mentor) or wen (mentor)
Differential to be added to commit message

Test Plan

portlint -C: looks fine
Passed poudriere {10.3,11.1}-{amd64,i386}
Tested in production by researchers

[jrm]

biology/fastqc/Makefile

4

The Porter's Handbook now promotes DISTVERSION usage and only setting PORTVERSION when the default value is incorrect. See https://reviews.freebsd.org/D11822. Sorry, we missed this in past reviews.

I think @mat would say DISTVERSIONPREFIX=v and then DISTNAME=${PORTNAME}_${DISTVERSIONPREFIX}${DISTVERSION}.

15–23

Blocks and order based on Chapter 14 of the PH? Maybe this? I will leave this to your discretion. Or, maybe @mat will chime in? Commenting on this can feel (to me) like overkill, but I also understand the motivation for more consistency across ports.

USES=		zip perl5 shebangfix
SHEBANG_FILES=	fastqc
USE_JAVA=	yes
USE_PERL5=	run

NO_ARCH=	yes
NO_BUILD=	yes
WRKSRC=		${WRKDIR}/FastQC

[mat]

biology/fastqc/Makefile

4

And then simply remove DISTNAME.

37–42

I think all these could be done at once:

	​        cd ${WRKSRC} && ${COPYTREE_SHARE} "Configuration Templates Help" \
	​                ${STAGEDIR}${DATADIR}

Same for the last three.

[jrm]

biology/fastqc/Makefile

4

I think you still need to set DISTNAME here because the default value has a - and not a _.

[jwb]

I think jrm is correct about DISTNAME.

For some reason, my checklist says NO_ARCH should come before USES. I added that item a while ago but did not document why. Probably a comment from a committer. It does seem to be the prevailing pattern in existing ports based on a quick grep -C.

I moved SHEBANG_FILES up next to USES where it belongs.

I think it would be nice if portlint mentioned these issues, assuming there's general agreement about them.

I updated my checklist to correspond with the other suggestions - thanks much.

[jwb]

Clean up per mentor suggestions.

[jrm]

I guess it depends whether NO_ARCH and NO_BUILD should be part of the block described in 15.5 of the PH. If they do belong there, a portlint update would be helpful. I think all portlint changes are up to marcus@.

[jwb]

That would seem like the logical place for NO_ARCH, at least. I could not find anything specific in the guide. Sec. 13.13 is a 1-liner...