Phd2fasta is distributed together with sci-biology/phred and sci-biology/phrap under same license. Quoting from INSTALL file: Phd2fasta: Phred and consed write sequence and quality value information in 'phd' output files. A phd file contains information in a header, the called bases, the base quality values, and the base call trace locations. Phd2fasta reads phd files and writes sequence and quality value FASTA files, which phrap and cross_match need as input. (Consed needs phd files in order to obtain the base call locations.) # equery files phd2fasta [ Searching for packages matching phd2fasta... ] * Contents of sci-biology/phd2fasta-20080822: /usr /usr/bin /usr/bin/phd2fasta /usr/share /usr/share/doc /usr/share/doc/phd2fasta-20080822 /usr/share/doc/phd2fasta-20080822/phd2fasta.txt.bz2 #
Created attachment 177015 [details] phd2fasta-20080822.ebuild
$ /usr/bin/phd2fasta -help parameter argument default description --------- -------- ------- ----------- -if <filename> none read input filenames from file -id <dirname> none read input files from <dirname> -ix <filename> none read exclude filenames from file -is none none read filenames from stdin -os <filename> none sequence output filename -oq <filename> none quality output filename -ob <filename> none base position output file -oe <filename> none write edit file -of <filename> none write failure log -mask <type> none mask vector (types: vector sequencing cloning all) -halt none none exit on file read/process error -verbose none none Display some processing information. -V none none show version -help none none help -h none none help -doc none none show documentation no input files specified no output file specified $ /usr/bin/phd2fasta -V phd2fasta version: 0.990622.f no input files specified no output file specified $ I got the dates from the tar archived file mtimes but while reading docs for sci-biology/consed we will have to check for the version in this format: 0.990622.f. So, this ebuild should be named phd2fasta-0.990622.f.ebuild. Or I would prefer to keep the archive file dates and runa runtime check for version of tools required. Or just ignore. It is nasty. consed sources contain also the phd2fasta sourcecode so both packages will have file collision and newer version of colliding files will be preferred/required.
OK, name it phd2fasta-0.990622.ebuild instead. Do not know what the ".f" means. Other packages from same team contain e.g. ".bcd".
Created attachment 177104 [details] Manifest
No comments have been made on this bug report for some time. Is anyone still interested in integration of this package? If yes, please indicate that here in this bug report. Otherwise we'll resolve the bug in the near future, since sci(-*) has an extremely large number of pending package requests and we would like to focus...
No response for six weeks. Resolving...
(In reply to comment #5) > No comments have been made on this bug report for some time. > Is anyone still interested in integration of this package? > > If yes, please indicate that here in this bug report. Seems I already put it into consed package in Gentoo in the past: ;-) # equery belongs phd2fasta * Searching for phd2fasta ... sci-biology/consed-19-r2 (/usr/bin/phd2fasta) # /usr/bin/phd2fasta -help parameter argument default description --------- -------- ------- ----------- -if <filename> none read input filenames from file -id <dirname> none read input files from <dirname> -ix <filename> none read exclude filenames from file -is none none read filenames from stdin -os <filename> none sequence output filename -oq <filename> none quality output filename -ob <filename> none base position output file -oe <filename> none write edit file -of <filename> none write failure log -mask <type> none mask vector (types: vector sequencing cloning all) -halt none none exit on file read/process error -verbose none none Display some processing information. -V none none show version -help none none help -h none none help -doc none none show documentation no input files specified no output file specified #
Grrh, # ls -la /usr/share/doc/phd2fasta-* ls: cannot access /usr/share/doc/phd2fasta-*: No such file or directory # ls -la /usr/share/doc/consed-19-r2/ total 160 drwxr-xr-x 2 root root 4096 Dec 6 12:58 . drwxr-xr-x 1553 root root 69632 Jan 4 01:39 .. -rw-r--r-- 1 root root 3257 Dec 6 12:55 19.0_announcement.txt.bz2 -rw-r--r-- 1 root root 74865 Dec 6 12:55 README.txt.bz2 # While taking into account we install whatever phd2fasta version was current when consed was released, I would have preferred individual phd2fasta package, or at least the docs installed from the separate bundle.
