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id 5AFCD18874 for ; Sat, 5 Apr 2014 13:21:08 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1396703965.ae0815f92cc318782734d09b18d0cf78f564c8bb.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/consed/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/consed/ChangeLog sci-biology/consed/consed-20-r1.ebuild sci-biology/consed/consed-21.ebuild sci-biology/consed/consed-22.ebuild sci-biology/consed/consed-23.ebuild sci-biology/consed/consed-24.ebuild sci-biology/consed/consed-25.ebuild sci-biology/consed/consed-26.ebuild sci-biology/consed/consed-27.ebuild X-VCS-Directories: sci-biology/consed/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: ae0815f92cc318782734d09b18d0cf78f564c8bb X-VCS-Branch: master Date: Sat, 5 Apr 2014 13:21:08 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 4a3b3efe-5661-4c7c-a2b6-3cd7bbe4d38f X-Archives-Hash: 0f37bb0e8bb0dfc142ed3133b12e2b1f commit: ae0815f92cc318782734d09b18d0cf78f564c8bb Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Sat Apr 5 13:19:25 2014 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sat Apr 5 13:19:25 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ae0815f9 sci-biology/consed: add a stub file for consedrc; refer to it via CONSED_PARAMETERS Package-Manager: portage-2.2.7 --- sci-biology/consed/ChangeLog | 6 ++++++ sci-biology/consed/consed-20-r1.ebuild | 3 +++ sci-biology/consed/consed-21.ebuild | 3 +++ sci-biology/consed/consed-22.ebuild | 3 +++ sci-biology/consed/consed-23.ebuild | 3 +++ sci-biology/consed/consed-24.ebuild | 3 +++ sci-biology/consed/consed-25.ebuild | 3 +++ sci-biology/consed/consed-26.ebuild | 3 +++ sci-biology/consed/consed-27.ebuild | 3 +++ 9 files changed, 30 insertions(+) diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog index ed7f9c8..4bbf7b9 100644 --- a/sci-biology/consed/ChangeLog +++ b/sci-biology/consed/ChangeLog @@ -5,6 +5,12 @@ 05 Apr 2014; Martin Mokrejs consed-20-r1.ebuild, consed-21.ebuild, consed-22.ebuild, consed-23.ebuild, consed-24.ebuild, consed-25.ebuild, consed-26.ebuild, consed-27.ebuild: + sci-biology/consed: add a stub file for consedrc; refer to it via + CONSED_PARAMETERS + + 05 Apr 2014; Martin Mokrejs consed-20-r1.ebuild, + consed-21.ebuild, consed-22.ebuild, consed-23.ebuild, consed-24.ebuild, + consed-25.ebuild, consed-26.ebuild, consed-27.ebuild: sci-biology/consed: fix more hardcoded paths 02 Apr 2014; Martin Mokrejs consed-20-r1.ebuild, diff --git a/sci-biology/consed/consed-20-r1.ebuild b/sci-biology/consed/consed-20-r1.ebuild index 7f7ddc1..30ba866 100644 --- a/sci-biology/consed/consed-20-r1.ebuild +++ b/sci-biology/consed/consed-20-r1.ebuild @@ -64,6 +64,9 @@ src_install() { align454reads align454reads_answer solexa_example \ solexa_example_answer selectRegions selectRegionsAnswer || die echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed" + echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed" + mkdir -p "${D}"/etc/consedrc + touch "${D}"/etc/consedrc doenvd "${S}/99consed" || die sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die diff --git a/sci-biology/consed/consed-21.ebuild b/sci-biology/consed/consed-21.ebuild index 77ec1a2..b7993b7 100644 --- a/sci-biology/consed/consed-21.ebuild +++ b/sci-biology/consed/consed-21.ebuild @@ -64,6 +64,9 @@ src_install() { align454reads align454reads_answer solexa_example \ solexa_example_answer selectRegions selectRegionsAnswer || die echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed" + echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed" + mkdir -p "${D}"/etc/consedrc + touch "${D}"/etc/consedrc sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die diff --git a/sci-biology/consed/consed-22.ebuild b/sci-biology/consed/consed-22.ebuild index e7c9186..4c8dd7f 100644 --- a/sci-biology/consed/consed-22.ebuild +++ b/sci-biology/consed/consed-22.ebuild @@ -64,6 +64,9 @@ src_install() { align454reads align454reads_answer solexa_example \ solexa_example_answer selectRegions selectRegionsAnswer || die echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed" + echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed" + mkdir -p "${D}"/etc/consedrc + touch "${D}"/etc/consedrc doenvd "${S}/99consed" || die sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die diff --git a/sci-biology/consed/consed-23.ebuild b/sci-biology/consed/consed-23.ebuild index e7c9186..4c8dd7f 100644 --- a/sci-biology/consed/consed-23.ebuild +++ b/sci-biology/consed/consed-23.ebuild @@ -64,6 +64,9 @@ src_install() { align454reads align454reads_answer solexa_example \ solexa_example_answer selectRegions selectRegionsAnswer || die echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed" + echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed" + mkdir -p "${D}"/etc/consedrc + touch "${D}"/etc/consedrc doenvd "${S}/99consed" || die sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die diff --git a/sci-biology/consed/consed-24.ebuild b/sci-biology/consed/consed-24.ebuild index e7c9186..4c8dd7f 100644 --- a/sci-biology/consed/consed-24.ebuild +++ b/sci-biology/consed/consed-24.ebuild @@ -64,6 +64,9 @@ src_install() { align454reads align454reads_answer solexa_example \ solexa_example_answer selectRegions selectRegionsAnswer || die echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed" + echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed" + mkdir -p "${D}"/etc/consedrc + touch "${D}"/etc/consedrc doenvd "${S}/99consed" || die sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die diff --git a/sci-biology/consed/consed-25.ebuild b/sci-biology/consed/consed-25.ebuild index e7c9186..4c8dd7f 100644 --- a/sci-biology/consed/consed-25.ebuild +++ b/sci-biology/consed/consed-25.ebuild @@ -64,6 +64,9 @@ src_install() { align454reads align454reads_answer solexa_example \ solexa_example_answer selectRegions selectRegionsAnswer || die echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed" + echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed" + mkdir -p "${D}"/etc/consedrc + touch "${D}"/etc/consedrc doenvd "${S}/99consed" || die sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die diff --git a/sci-biology/consed/consed-26.ebuild b/sci-biology/consed/consed-26.ebuild index e7c9186..4c8dd7f 100644 --- a/sci-biology/consed/consed-26.ebuild +++ b/sci-biology/consed/consed-26.ebuild @@ -64,6 +64,9 @@ src_install() { align454reads align454reads_answer solexa_example \ solexa_example_answer selectRegions selectRegionsAnswer || die echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed" + echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed" + mkdir -p "${D}"/etc/consedrc + touch "${D}"/etc/consedrc doenvd "${S}/99consed" || die sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die diff --git a/sci-biology/consed/consed-27.ebuild b/sci-biology/consed/consed-27.ebuild index e7c9186..4c8dd7f 100644 --- a/sci-biology/consed/consed-27.ebuild +++ b/sci-biology/consed/consed-27.ebuild @@ -64,6 +64,9 @@ src_install() { align454reads align454reads_answer solexa_example \ solexa_example_answer selectRegions selectRegionsAnswer || die echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed" + echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed" + mkdir -p "${D}"/etc/consedrc + touch "${D}"/etc/consedrc doenvd "${S}/99consed" || die sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die