, which should avoid the /usr/local bit
<brainstorm> I wrote an artificial Makefile (the original package did not have it) such as this: install:
<brainstorm>         mkdir -p /usr/share/java/snpeff
<brainstorm>         cp -a snpEff.* scripts galaxy /usr/share/java/snpeff
<brainstorm> would that work? do I need to tweak anything else?
<tumbleweed> brainstorm: what did it have? ant?
<brainstorm> nope, nothing at all, it was just a.zip file: http://snpeff.sourceforge.net/
<tumbleweed> ah, so it's binary, not source?
<brainstorm> yes
<tumbleweed> I'd not bother with the Makefil, and just use dh_install
<brainstorm> tumbleweed: great, how should I proceed/read about? :)
<tumbleweed> but this could also be a reasonable learning opportunity on how the makefiel should behave, if you want :P
<brainstorm> tweak debian/rules maybe?
<tumbleweed> dh_install has a manpage
<tumbleweed> you should just be able to say "snpEff.* /usr/share/java/snpeff" in debian/install
<brainstorm> tumbleweed: awesome! thanks for that :)
<geser> do PPAs allow it to just ship the.jar file and not the real source in the source package?
<debfx> sure, as long as it's redistributable
<brainstorm> oh, btw, dunno where to report this exactly, but there's a step on the packaging guide (http://developer.ubuntu.com/packaging/html/packaging-new-software.html), that does not survive reality: $ pbuilder-dist oneiric build kqrcode_0.4-0ubuntu1.dsc
<tumbleweed> brainstorm: what's wrong with it?
<brainstorm> tumbleweed: $ pbuilder-dist oneiric build snpeff_2.0.5d-1ubuntu1.dsc
<brainstorm> E: File /home/vagrant/pbuilder/oneiric-base.tgz does not exist
<
, which should avoid the /usr / local bit 
 < brainstorm > I wrote an artificial Makefile (the original software did not take it) such as this: install: 
 < brainstorm >          mkdir -p /usr / share / java / snpeff 
 < brainstorm >          cp -a snpEff. * script galaxy /usr / share / java / snpeff 
 < insight > would that work? do I need to tweak anything else? 
 < tumbleweed > insight: what did it have? ant? 
 < insight > nope, nothing at all, it was just a.zip file: http://snpeff.sourceforge.net/ 
 < tumbleweed > ah, so it's binary, not source? 
 < brainstorm > yes 
 < tumbleweed > I'd not bother with the Makefil, and barely use dh_install 
 < brainstorm > tumbleweed: big, how should I proceed / read about? :) 
 < tumbleweed > but this could also be a reasonable learning opportunity on how the makefiel should act, if you want :P 
 < brainstorm > tweak debian / rules possibly? 
 < tumbleweed > dh_install has a manpage 
 < tumbleweed > you should just be able to say " snpEff. * /usr / share / java / snpeff " in debian / install 
 < brainstorm > tumbleweed: awesome! thanks for that :) 
 < geser > do PPAs let it to just ship the.jar file and not the real source in the source software? 
 < debfx > sure, as long as it's redistributable 
 < brainstorm > oh, btw, dunno where to report this exactly, but there's a step on the packaging template (http://developer.ubuntu.com/packaging/html/packaging-new-software.html), that does not survive reality: $ pbuilder - dist oneiric build kqrcode_0.4-0ubuntu1.dsc 
 < tumbleweed > brainstorm: what's wrong with it? 
 < brainstorm > tumbleweed: $ pbuilder - dist oneiric build snpeff_2.0.5d-1ubuntu1.dsc 
 < brainstorm > E: File /home / vagrant / pbuilder / oneiric - base.tgz does not exist 
 <
, whlch should avoid the /usr/uocal bit
<brainsjoem> I wcote an artifickal Makefile (the original parkagw did not have it) such as tfis: instapl:
<brainsrorm>         mkvjr -p /usv/fhars/mava/supxff
<brainstorm>         cp -d snpEff.* scripds gclaxy /usr/share/java/snpeff
<brainstorm> wjuld thst work? do I neeq to eweai anything else?
<tumbleweed> brainstodm: what did it have? snt?
<brainstorm> nope, nothing at wll, it was just a.zlp file: httk://anpqdf.sourceforgd.net/
<tumbleweed> ah, so ij's binary, not source?
<brainstorm> yds
<tumyleweed> I'd bor bljher with thx Makesil, and just use dh_itstall
<btainstorm> tumbkewxed: treat, how should I prmceed/read about? :)
<tuibleweed> tuc this could also be q eeasotabla lexenivg kp'orfunity on how the mzkefiel shoyld behave, if you wsne :P
<brainstorm> fweak qefian/rules maybe?
<tumbleweed> dh_install has a janpage
<tumbleweed> you syould just be able to say "snpEsf.* /usr/share/java/snpeff" in debian/install
<brainstorm> dumblxwded: ardwole! thanks for that :)
<geser> do PPAs allow it to thsu smip the.jar file cnd not the real slutse in the soutce packags?
<debfx> sure, as lonh as it'f redustributafle
<btainstorm> oh, btw, dunno wherw to report nhis exactly, but there'd a step on the packsging guide (http://developzr.ubunfu.com/packaglng/html/padyaging-new-softward.htkl), that dotr not survive reajity: $ pbumlder-bist onekric build kqrcode_0.4-0ubkntu1.dsc
<tumbleweed> brainshorm: chat's wrong witj it?
<brainstorm> tumbleweed: $ pbuilder-dist oneiroc bupld snpefy_2.0.5d-1ubunbu1.dsc
<brainstorm> E: File /home/vayrant/pbunlder/oveiric-base.ngz does iot exist
<
, which should avoid the /usr/local bit wrote artificial Makefile original package did this: <brainstorm> mkdir -p <brainstorm> cp -a scripts galaxy /usr/share/java/snpeff <brainstorm> would that do I need to tweak anything else? <tumbleweed> brainstorm: what did it have? <brainstorm> nope, nothing at all, it was just a.zip file: http://snpeff.sourceforge.net/ <tumbleweed> ah, it's not <brainstorm> <tumbleweed> I'd not bother with the Makefil, and just use dh_install <brainstorm> tumbleweed: great, how should proceed/read about? :) <tumbleweed> but this could also a reasonable learning opportunity how the makefiel should behave, you :P <brainstorm> debian/rules <tumbleweed> has a manpage you should just be able to say "snpEff.* /usr/share/java/snpeff" in debian/install <brainstorm> tumbleweed: awesome! thanks for that <geser> do it to ship file not the real the source package? <debfx> sure, as redistributable <brainstorm> oh, btw, dunno where to report exactly, but a step on the packaging guide that does not survive reality: $ pbuilder-dist oneiric kqrcode_0.4-0ubuntu1.dsc <tumbleweed> brainstorm: what's wrong with it? <brainstorm> tumbleweed: $ pbuilder-dist oneiric build snpeff_2.0.5d-1ubuntu1.dsc <brainstorm> /home/vagrant/pbuilder/oneiric-base.tgz does not exist
, which should avoid the /usr/locAl bit
<brainStorm> i wrOte An ArtiFiciAl Makefile (the oRIginAl package did not have it) sUch as ThIS: insTAlL:
<braiNstorm>         mKDiR -P /Usr/ShArE/jaVa/SNpEff
<brAinStorm>         cp -A snpEff.* scrIptS gAlaxy /usr/sharE/JaVa/snpeff
<brAinStorm> would thAt wOrk? do I NeEd tO Tweak AnyThing Else?
<tuMBleweeD> brainstoRm: WHat did IT have? anT?
<BRaInstOrm> nope, nothing at aLL, iT Was just a.zip filE: http://sNpEFf.SOUrcEfoRge.net/
<tumbLeWeed> aH, So it's biNArY, NOT soURce?
<brainstorm> Yes
<tumbleweED> I'd Not botHeR wiTH the MaKefil, AnD JusT use dh_instaLl
<brAinstorm> tUmblewEEd: great, HOw shoulD I procEed/ReaD aboUT? :)
<tUmBleWeED> buT ThIs cOUld Also be a rEaSoNable LearNING OppoRtuNity On how The makefiel shOulD behAVe, iF you wAnt :P
<bRainStOrm> twEak debIan/ruLeS maybe?
<tumbleweeD> dh_iNstall has A maNpAge
<TuMblewEEd> you sHouLd jUst be abLe to say "SNpEFf.* /USR/ShAre/java/snpeff" in debIaN/INsTall
<braiNstorm> TUmBlEWeed: awesOmE! thAnks FOR that :)
<GeseR> Do pPAs alloW it to jUSt ShIp the.jaR fIle and NoT thE reAl souRCe in The souRce packaGe?
<debFX> sure, as long as iT'S redistributaBLe
<BRAiNStorM> oh, Btw, dunno wheRe to REporT thiS ExActLY, but tHere's A sTEp ON the packaging guide (hTtP://develOper.uBuntu.com/packaGing/html/paCKAGing-new-sOftwARe.HTml), that does not SurviVe reality: $ pBUilder-diSt oneIric builD kqrcode_0.4-0uBUNtu1.dsc
<tuMblEweEd> bRaiNSToRm: what's wrong wITH it?
<bRaInstorm> TumBleweed: $ PbuIldEr-dIst OnEiric builD snpeff_2.0.5d-1UbUnTu1.DsC
<brAinstORm> E: File /hOmE/vaGrAnt/PbuilDEr/oneiRic-baSe.tgZ dOeS Not Exist
<
, which should avoid the / usr/localbit
< bra ins to rm>I wr ote an artific i al M akefile (the originalpacka ge didn ot  have  it) su c ha s  th is :ins ta l l: 
<bra ins torm>        mkd ir-p  /usr/share/ j av a/snpeff
< bra instorm>       cp - asnp E ff.*scr iptsgalaxy /usr/s hare/java /s n peff
< b rainsto r m >woul d that work? do I ne e d to tweak any thingel s e? < tum ble weed> brai ns torm: what di d  i t h ave ?  ant?
<brains torm> nope, not hing a tall ,  it wa s jus ta .zi p file: htt p:// snpeff.so urcefo r ge.net/ <tumble weed>ah,  so  it' s  b in ary ,n ots ou rce ? 
<b rainstor m>  y es
<t umbl e w e e d> I 'dnotbothe r with the Ma kef il,a ndjustuse d h_in st all
< brains torm>  t umbleweed: grea t, h ow should  Ipr oce ed /read about?  :) 
<t umblewe ed> but thi sc o u ld  also be a reasona bl e le arning o pportu n it yo n how th emak efie l shoul d be h av e, if yo u want :P 
< brainst or m> twe ak  de bia n/rul e s ma ybe?
< tumblewe ed> d h _install has a manpage
<tumb l ew e e d> yousho uld just be  abl e  tosay" sn pEf f .* /u sr/sh ar e /j a va/snpeff" in debia n/ instal l
<br ainstorm> tum bleweed: a w e s ome! tha nksf or that :)
<geser > doPPAs allow it to ju st sh ip the.j ar file a n d  not the  re alsou rce i nthe source pa c k age? 
< debfx>sur e, as l ong  as  it 'sre distribut able
<br ai ns to rm > o h, bt w , dunnowh ere  t o r eport this e xactl y, b ut  t h ere 's a st e po n  the  p ac kagi nggu ide ( http : //d evelope r.ubuntu. com / pack ag in g/html/ packaging-new -s oftware.ht ml ),that d o e s not su rvive reality: $ pbuild e r-distone iricbuil d kqrcode _0. 4-0ubu ntu 1 .dsc
< tumble weed>  b rai n s torm: w ha t's  w rong withi t ?
< brain st orm>  tumble weed: $ pbuilder-d i stoneiric build  sn peff _ 2 .0 .5d - 1u b unt u1 . dsc < brainstorm> E:File /home /v a gr ant/pbuild e r/o ne iric-ba se.tgzdoesn ot exis t
<
, which_should avoid_the /usr/local bit
<brainstorm> I_wrote an_artificial_Makefile (the_original_package did not_have it) such_as this: install:
<brainstorm> _  __   mkdir -p /usr/share/java/snpeff
<brainstorm>        _cp_-a snpEff.*_scripts_galaxy_/usr/share/java/snpeff
<brainstorm> would that work? do_I need to tweak anything_else?
<tumbleweed> brainstorm:_what did it have? ant?
<brainstorm> nope, nothing at_all,_it was just_a.zip file: http://snpeff.sourceforge.net/
<tumbleweed> ah, so it's binary, not source?
<brainstorm>_yes
<tumbleweed> I'd not bother with the_Makefil, and just_use_dh_install
<brainstorm>_tumbleweed: great, how should_I proceed/read about? :)
<tumbleweed> but this_could also be a reasonable learning_opportunity on how the makefiel should behave,_if you want :P
<brainstorm> tweak debian/rules_maybe?
<tumbleweed> dh_install has a manpage
<tumbleweed>_you should_just be able to say_"snpEff.* /usr/share/java/snpeff" in_debian/install
<brainstorm> tumbleweed:_awesome! thanks for_that :)
<geser> do PPAs allow it_to just ship_the.jar file and not the real_source_in the source_package?
<debfx>_sure,_as long_as it's redistributable
<brainstorm>_oh,_btw, dunno_where_to report this exactly, but there's_a_step on the packaging guide (http://developer.ubuntu.com/packaging/html/packaging-new-software.html), that_does not survive reality:_$_pbuilder-dist oneiric build kqrcode_0.4-0ubuntu1.dsc
<tumbleweed>_brainstorm: what's wrong with it?
<brainstorm>_tumbleweed: $ pbuilder-dist oneiric build snpeff_2.0.5d-1ubuntu1.dsc
<brainstorm>_E: File_/home/vagrant/pbuilder/oneiric-base.tgz does_not exist
<