pkgsrc-Bugs archive

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index][Old Index]

pkg/47588: mira-3.9.9



>Number:         47588
>Category:       pkg
>Synopsis:       mira-3.9.9
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    pkg-manager
>State:          open
>Class:          change-request
>Submitter-Id:   net
>Arrival-Date:   Sun Feb 24 01:45:00 +0000 2013
>Originator:     Thomas Vaughan
>Release:        NetBSD 6.0.1 (GENERIC) i386
>Organization:
Public Health England
>Environment:
NetBSD Temaraire 6.0.1 NetBSD 6.0.1 (GENERIC) i386
>Description:
Information for mira-3.9.9:

Comment:
Genome and EST Sequence Assembly System

Requires:
tcl-8*
{gcc47,gcc47-libs}>=4.7
{gcc47,gcc47-libs}>=4.7.0
boost-libs-1.52.*
boost-libs>=1.51.0

Description:
MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome and
EST projects. MIRA assembles reads gained by

* electrophoresis sequencing (aka Sanger sequencing)

* 454 pyrosequencing (GS20, FLX or Titanium)

* Ion Torrent

* Solexa (Illumina) sequencing

* (in development) Pacific Biosciences sequencing

into contiguous sequences (called contigs). One can use the sequences of
different sequencing technologies either in a single assembly run (a true
hybrid assembly) or by mapping one type of data to an assembly of other
sequencing type (a semi-hybrid assembly (or mapping)) or by mapping a data
against consensus sequences of other assemblies (a simple mapping).

Homepage:
http://sourceforge.net/apps/mediawiki/mira-assembler
>How-To-Repeat:
(New package seems to be fully functional; pkgsrc version is 2012Q4)
>Fix:
begin 644 mira.tar.gz
M'XL(`))J*5$"`^U:^U/C.!+F5_Q7J`*U`PMV_,YC+U,3DI!)+239.&QQ55N5
MDFW9T>'7V@J/I?C?KV7G!0/+[-X,4[?CKP#;ZE9+EO1UMV1"FN*=KPQ9UN6:
M8<!55FJ&S*\<JVM^KZB*HJJF;BH:E"M0Q=@Q=MX`BXSA%*$=]HK>S9R08.<?
MAQ#FOYI@YLQ)]NWG7S6,7*XH>DTIY_^-Y[^XBEGJS'CQ+&,IC7PGCABF$4FE
MCW]W_H'.IJZ_./^&H?'YEW55KIDUKJ="H;DCE_/_U;$_).S$ZNX+0OLZIBZJ
MD#2-TR9ZE[#4I9XW8^_0#<Y0%#/D$B?`*7$1C1";TPQE3IR0"@(QN4T"ODBX
M3)@SEC2K5=]Q)#]:2''J\WM1E\QJ$J<,UM2,Q=*<A8$@B**(8,%5\W7XR8*#
MNM3?565%%?F/@E2Y:1A-59;6G@,=\;_"T='1G]@1/GQ`HMHX-M$1_*VA#Q\$
MM.<2#Z2H6.M67J6SJC*;SP0$.C1R@H5+T+]H#$8)#M\+1YM")V,N6'G_2+4"
MA7`/G0B619GTL0(J_T_\7S`:P,!DCM3Y`O[_%?YS7[_BOV'F\=\P%;WD_[?D
M/URC^'7N`]V]1>0P&D?H76[!]SRM2YS8)0?`P(RA@HT_',.-VVPNGP[?;;C/
M%UNU6&Q_G?!;E7.6:SG+M17+'[/8>X;$^8M*\_=/=(N!F./(!1K[U4=/G,_?
M0?Q/<(I#PDB:_6]>X#7^FZ:>YW^RH6B&R?-$I08Y0,G_-^7_*;T%9A.4I+$=
MD!"YP*E%E@'E,5N%])N;&\E+82!HQK(\L"<0%_.@.V,XN*K.J3\/[E*2$$89
MO28B%P$GQ1!'U",9.U:?Q/SM1?8WP_VVB<('&*H*_#_*KR;X`91[IO/!I#U>
MZS:;4"\C![3P">@'1+-C`>U6?HM^8Z+U<S.,TM8=R9I1FK84N5*(EI>9U1[V
M>Y.9U9M.!\.^51'$9<5^KPDNB5>LK(VUK>8B=9VPI4CJIK1SUDRN`R=O([EV
MP@!OF@%Q=PR52"[U"$U:<C/(+U_6]3S#?_#:'O6A[2^V__MS_BNZJC[=_^D&
M[/]+_K]I_'>!Z2@B-^@:IQ2##SA&^_=GO<N3MM4;ML][#\>(Q0@'07R#O#@M
MA`]HF69#6(3JWB(($"RC><'R]5)Z@=F:\BRSU]5R-BL-6#R<SL5-G?.9./,8
M58Y>!01T)'XY?'%S7D!N_3AVK\$A00K5JBRBJRB^`3<C4@\Q<)BH4HQS!;50
MA:M7?N)N.A*.5@J7E<?3Q#4O"R7TC&AE[R?DT8V1YQ2W6T,(W:-]G,V*D>=W
M(6GNW\,5,B(2Q>+^V6#8&XX>F@A\B7/%UP-?)=P(6KX>3&P(BX/"VD(WE,US
MCUQ![W\PA+7M&73ZKQF0)`EQ(^9/Z('W<P^J\47*#?"^H6P.+C\@61;<00X:
M!S`N7AJ'>;0;?QPC>T$#%U:M<X5](NQ\5\C]_SF^@KUP0+Y2&Z_X?U57E*WS
MW^+\SS#*_=];8`^M(\">('0'UI3SO[5;Y&U20VH(G?:TUQ]-!CVKM6O3.(C]
M.^&\;4UY^C.8\M+]^ZWGF36ZF'1ZIZ,)I$*MW`Z&-#($SJ;5!Z%W.9VT.].9
M=7%ZV=J58/`E^P]("L_;@^$4?GN3UFYRY4-R)RXR8/V'HGL\V10^CLY[XW8?
MNK?,1[-XD3H$O(1/I(BP*DZ2K!H2E^(;>D6KCQL7.J/S\]YPVMKM@[\*"8+=
M'.I94V21WQ<D<@AJ%ZIWR+K+&`F%LT&G-[2@.3]:B'X2B-?0T?'/_5D7JG4'
M\+X7X_%H`A9Y5T67\*.?5!`NK-YL.AJ=64>MW5T_!':AA*2!T.]T9I/>+UTH
MU253$/K#BUEG-#P=]"\FT`JD>GG5L\$)K[U5`,GF!;PW#+6#'(AJ0N_7]MEL
M/.F=#BYY&Z?@NZ$_+>XKA;7%66_X*Y>"L+5_O]1I_O)0M6E4?5%U%0->,,;-
MC,?/VX.>/>D8Z+;Y2+7(+?CM+6OM29^/CBAR-R[F4K"Y4@>C3RV=C$;YF+?L
M&+8<8D#M[$5SN0J86]7AYH23B\%9%V9NW!MV\XGA/7[?4B5#TK2F)%7AQR77
M)"B&YA/U:QJ*$$E2\KZE_+C4AY7&XC2KKF7"5@7F!&)]I1G@R*]"B2!(ZQ.&
M[38W;U7-PQ$$KBM-"J\J?ZH_)]@%CGQ>%?Y:KVDR<LM@`^A4\QEY33N\JMJ9
M*R4I\;)<86\/C0/LD'D<0+^*\+U@D,BAO&8>PF,/0<;C!SDG/!;'0<8/E0K.
M-]&]L"=!4K)_/QI;_[8>4`L2D3,:+6XK7/#<>_EK.T_[NR>1R*4>[];#BYV_
M\G/=G>\3>?P?GX'?_XK??U\[_U%KR_-?!51K^???FE:>_[P%/D!&'9*(;=(`
M[LQA`P89-YN!*_@/<5A>YF$8*=5+L2]Q/[8NRB"U=MCC,L[&]=/O3S7H;;O3
MT_GA,''7I7PAKF\L@E-G#D'6&HZS=:D3T&3]$$)\YO>9DW-?R-UO<1[DDC#.
MSX3`,X7;@FR1\`]0,RUU0<[N9H77Z$_;_>[)9RA.>NWN>>\S%(MW2QU)T23Y
ML_49]B$`2.R6"6_+?TAG.I-OQG]%W7S_-31#*?C/Y27_OSKX!AK1#&$4+@)&
MQ0329=0=ME&V2HI=S##:9/`AY-C+T'X#89X@?YU,"SR97KJ,3,KWYNN*&4HA
M5\F07WPEMN\$X4>4^X4T3N9Q2C+^3:EHDV_<#_`51A8D3=#6IOB0U](-'25W
M:;RMW;=4^1B=GETBZ->4,AS119AK#R#EF,9I"CZ./UK0Y5N,#@9!L`AIA`^W
MK'/Y`:0B>5H1)]PM'J(Q=JA''71"X\RA?$2R1U5HQ.+\#(SZBWBQEH'6@8.#
M`-ZU$&:'$AI%!#DX0K!;R`\?-KJQ)_"O[81W<WL8&''F$=]R45`BD-O"<$`/
M,<I`"H./5SN6=!'!F"&6+H@PO[-3ZJYEAWQ,[#O$9X[;C*$7["XA/!/+)Y>?
MZD4;4U`<\X:$[7YP?;`/*E1\8A\=@/VE\<.GC>&\"0'S><\8RAU=E#T:IU5[
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MXB8AXX&Z=:..83Q5S5`)KNF*9NO8-5S;UFU%=1J.@S\QN?7/.4L[9JUNJIK9
M,%73EDU%]V35-`RB:375;*BN[6"W42\=:(D2)4J4*%&B1(D2)4J4*%&B1(D2
>)4J4*%&B1(D2)4J4*%&B1(D2_S#\%[;PPJ4`4```
`
end



Home | Main Index | Thread Index | Old Index