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| author |   Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-05-22 16:28:52 +0200 |
|---|---|---|
| committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-05-22 16:28:52 +0200 |
| commit | 671a7fde681f15efe6ee2168e0c901a8306d5331 (patch) | |
| tree | cbc0d454d80dfb0aeff126551a1a97ffd78720d2 | |
| parent | Drop obsolete mask (diff) | |
| download | sci-671a7fde681f15efe6ee2168e0c901a8306d5331.tar.gz sci-671a7fde681f15efe6ee2168e0c901a8306d5331.tar.bz2 sci-671a7fde681f15efe6ee2168e0c901a8306d5331.zip | |
sci-biology/SOAPdenovo2: add Debian manpage
https://manpages.debian.org/testing/soapdenovo2/soapdenovo2.1.en.html
Package-Manager: Portage-2.3.5, Repoman-2.3.2
| -rw-r--r-- | sci-biology/SOAPdenovo2/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild | 7 | ||||
| -rw-r--r-- | sci-biology/SOAPdenovo2/files/soapdenovo2.1 | 22 |
3 files changed, 25 insertions, 5 deletions
diff --git a/sci-biology/SOAPdenovo2/Manifest b/sci-biology/SOAPdenovo2/Manifest deleted file mode 100644 index 02b7d47c9..000000000 --- a/sci-biology/SOAPdenovo2/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST SOAPdenovo2-src-r240.tgz 1539853 SHA256 b58fdb9b14766a122992d23dba5e91bd733c86e0062b432181aa5c1e7f052bb7 SHA512 1e420ba7526887d8a390a1ea6dce369aee428d8cd2f11b1725a32b971ddd7686180012b10723803a5c5053605141a999379acf06cf8468ac462424fed78e4ff2 WHIRLPOOL 819106c2cbc75401944b3358568a4f9c3a2df5bc472332e337ba493a6216c0383a01231427d4547a12de150a73be2551f44468a32fe22fb1349a5416f9dbe69c diff --git a/sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild b/sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild index 0ca68007a..affce03d3 100644 --- a/sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild +++ b/sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild @@ -5,11 +5,10 @@ EAPI=6 inherit toolchain-funcs -DESCRIPTION="Whole genome shotgun assembler (sparse de Bruijn graph)" -HOMEPAGE="https://sourceforge.net/projects/soapdenovo2 - https://github.com/aquaskyline/SOAPdenovo2 +DESCRIPTION="Whole genome shotgun assembler (sparse de Bruijn graph) (now MEGAHIT)" +HOMEPAGE="https://github.com/aquaskyline/SOAPdenovo2 http://gigascience.biomedcentral.com/articles/10.1186/2047-217X-1-18" -SRC_URI="https://sourceforge.net/projects/soapdenovo2/files/${PN}/src/r${PV}/${PN}-src-r${PV}.tgz" +SRC_URI="" LICENSE="GPL-3" SLOT="0" diff --git a/sci-biology/SOAPdenovo2/files/soapdenovo2.1 b/sci-biology/SOAPdenovo2/files/soapdenovo2.1 new file mode 100644 index 000000000..337618ace --- /dev/null +++ b/sci-biology/SOAPdenovo2/files/soapdenovo2.1 @@ -0,0 +1,22 @@ +.TH soapdenovo2 1 "February 09, 2013" "version 2.2.3" "USER COMMANDS" +.SH NAME +soapdenovo2 \- Short-read assembly method that can build a de novo draft assembly +.SH SYNOPSIS +.B soapdenovo_63mer soapdenovo_127mer + +.SH Introduction + +SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. + +1) Support large kmer up to 127 to utilize long reads. Three version are provided. + I. The 31mer version support kmer only <=31. + II. The 63mer version support kmer only <=63 and doubles the memory consumption than 31mer version, even being used with kmer <=31. + III. The 127mer version support kmer only <=127 and double the memory consumption than 63mer version, even being used with kmer <=63. + +Please notice that, with longer kmer, the quantity of nodes would decrease significantly, thus the memory consumption is usually smaller than double with shifted version. + +For more information, look at the MANUAL in /usr/share/doc/soapdenovo2 or on soapdenovo web site. + +.SH AUTHOR +Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging + |