ports/138262: [NEW PORT]biology/iolib:A general purpose trace file(and Experiment File) reading interface
Wen Heping
wenheping at gmail.com
Fri Aug 28 07:43:24 UTC 2009
>Number: 138262
>Category: ports
>Synopsis: [NEW PORT]biology/iolib:A general purpose trace file(and Experiment File) reading interface
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: change-request
>Submitter-Id: current-users
>Arrival-Date: Fri Aug 28 07:42:18 UTC 2009
>Closed-Date:
>Last-Modified:
>Originator: Wen Heping
>Release: FreeBSD 8.0-Current
>Organization:
ChangAn Middle School
>Environment:
FreeBSD fb8.wenjing.com 8.0-CURRENT FreeBSD 8.0-CURRENT #0: Sun Mar 22 22:12:06 CST 2009 root at fb8.wenjing.com:/usr/obj/usr/src/sys/GENERIC i386
>Description:
Io_lib is a library of file reading and writing code to provide a
general purpose trace file (and Experiment File) reading interface.
The programmer simply calls the (eg) read_reading to create a "Read"
C structure with the data loaded into memory. It has been compiled
and tested on a variety of unix systems, MacOS X and MS Windows.
WWW: http://staden.sourceforge.net/
>How-To-Repeat:
>Fix:
Patch attached with submission follows:
# This is a shell archive. Save it in a file, remove anything before
# this line, and then unpack it by entering "sh file". Note, it may
# create directories; files and directories will be owned by you and
# have default permissions.
#
# This archive contains:
#
# iolib
# iolib/Makefile
# iolib/distinfo
# iolib/pkg-descr
# iolib/pkg-plist
#
echo c - iolib
mkdir -p iolib > /dev/null 2>&1
echo x - iolib/Makefile
sed 's/^X//' >iolib/Makefile << 'b7ad3746b47ea4d30cc028e26598a798'
X# New ports collection makefile for: io_lib
X# Date created: 27 Aug, 2009
X# Whom: Wen Heping <wenheping at gmail.com>
X#
X# $FreeBSD$
X#
X
XPORTNAME= io_lib
XPORTVERSION= 1.12.1
XCATEGORIES= biology
XMASTER_SITES= SF
XMASTER_SITE_SUBDIR= staden/${PORTNAME}/${PORTVERSION}
X
XMAINTAINER= wenheping at gmail.com
XCOMMENT= A general purpose trace file(and Experiment File) reading interface
X
XUSE_AUTOTOOLS= libtool:22:env
XGNU_CONFIGURE= yes
XUSE_GMAKE= yes
XUSE_LDCONFIG= yes
X
XMAN1= srf_index_hash.1 srf_info.1 srf_list.1 illumina2srf.1 \
X srf2fasta.1 srf2fastq.1
XMAN3= read_scf_header.3 read_allocate.3 ExperimentFile.3 \
X write_reading.3 write_scf.3 read_deallocate.3 \
X fwrite_reading.3 read2scf.3 scf2read.3 \
X fwrite_scf.3 write_scf_header.3 read_reading.3 \
X read_scf.3 exp2read.3 fread_reading.3 \
X read2exp.3 fread_scf.3
XMAN4= Read.4
X
X.include <bsd.port.mk>
b7ad3746b47ea4d30cc028e26598a798
echo x - iolib/distinfo
sed 's/^X//' >iolib/distinfo << '6ece5bfd27be348ff9fef9c9bb26bcaf'
XMD5 (io_lib-1.12.1.tar.gz) = f511698b766d5bd7d15a8269bdcddf84
XSHA256 (io_lib-1.12.1.tar.gz) = 732fc729662f380861e12fd9006a1a1c072f459589b6d2c49a7c01c88a9cdf01
XSIZE (io_lib-1.12.1.tar.gz) = 772314
6ece5bfd27be348ff9fef9c9bb26bcaf
echo x - iolib/pkg-descr
sed 's/^X//' >iolib/pkg-descr << 'c04402d888d8b1769b87fa52eff5c855'
XIo_lib is a library of file reading and writing code to provide a
Xgeneral purpose trace file (and Experiment File) reading interface.
XThe programmer simply calls the (eg) read_reading to create a "Read"
XC structure with the data loaded into memory. It has been compiled
Xand tested on a variety of unix systems, MacOS X and MS Windows.
X
XWWW: http://staden.sourceforge.net/
c04402d888d8b1769b87fa52eff5c855
echo x - iolib/pkg-plist
sed 's/^X//' >iolib/pkg-plist << '0298aa480c8dd33592e6b51a7423979d'
Xinclude/io_lib/Read.h
Xinclude/io_lib/abi.h
Xinclude/io_lib/alf.h
Xinclude/io_lib/array.h
Xinclude/io_lib/compress.h
Xinclude/io_lib/compression.h
Xinclude/io_lib/deflate_interlaced.h
Xinclude/io_lib/error.h
Xinclude/io_lib/expFileIO.h
Xinclude/io_lib/fpoint.h
Xinclude/io_lib/hash_table.h
Xinclude/io_lib/io_lib_config.h
Xinclude/io_lib/jenkins_lookup3.h
Xinclude/io_lib/mFILE.h
Xinclude/io_lib/mach-io.h
Xinclude/io_lib/misc.h
Xinclude/io_lib/open_trace_file.h
Xinclude/io_lib/os.h
Xinclude/io_lib/plain.h
Xinclude/io_lib/scf.h
Xinclude/io_lib/scf_extras.h
Xinclude/io_lib/seqIOABI.h
Xinclude/io_lib/seqIOCTF.h
Xinclude/io_lib/sff.h
Xinclude/io_lib/srf.h
Xinclude/io_lib/stdio_hack.h
Xinclude/io_lib/tar_format.h
Xinclude/io_lib/traceType.h
Xinclude/io_lib/translate.h
Xinclude/io_lib/vlen.h
Xinclude/io_lib/xalloc.h
Xinclude/io_lib/ztr.h
Xbin/append_sff
Xbin/convert_trace
Xbin/extract_fastq
Xbin/extract_qual
Xbin/extract_seq
Xbin/get_comment
Xbin/hash_extract
Xbin/hash_list
Xbin/hash_sff
Xbin/hash_tar
Xbin/index_tar
Xbin/io_lib-config
Xbin/makeSCF
Xbin/scf_dump
Xbin/scf_info
Xbin/scf_update
Xbin/srf2fasta
Xbin/srf2fastq
Xbin/srf_dump_all
Xbin/srf_extract_hash
Xbin/srf_extract_linear
Xbin/srf_filter
Xbin/srf_index_hash
Xbin/srf_info
Xbin/srf_list
Xbin/trace_dump
Xbin/ztr_dump
Xlib/libstaden-read.a
Xlib/libstaden-read.la
Xlib/libstaden-read.so
Xlib/libstaden-read.so.1
X at dirrm include/io_lib
0298aa480c8dd33592e6b51a7423979d
exit
>Release-Note:
>Audit-Trail:
>Unformatted:
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