From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (2048 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id A2C03158451 for ; Tue, 9 Jan 2024 09:06:26 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id A00C02BC025; Tue, 9 Jan 2024 09:06:25 +0000 (UTC) Received: from smtp.gentoo.org (woodpecker.gentoo.org [140.211.166.183]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 817052BC025 for ; Tue, 9 Jan 2024 09:06:25 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 6AFCC343306 for ; Tue, 9 Jan 2024 09:06:24 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id A865D1437 for ; Tue, 9 Jan 2024 09:06:22 +0000 (UTC) From: "Anna Vyalkova" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Anna Vyalkova" Message-ID: <1704791162.8f10f75977eefa6285c362170df29351475f1ed7.cybertailor@gentoo> Subject: [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/files/ X-VCS-Repository: repo/proj/guru X-VCS-Files: sci-biology/cmdock/files/app_info_0.1.4.xml sci-biology/cmdock/files/cmdock-0.1.4-fix-detection.patch sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml X-VCS-Directories: sci-biology/cmdock/files/ X-VCS-Committer: cybertailor X-VCS-Committer-Name: Anna Vyalkova X-VCS-Revision: 8f10f75977eefa6285c362170df29351475f1ed7 X-VCS-Branch: dev Date: Tue, 9 Jan 2024 09:06:22 +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-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: fbe8f1aa-a3ca-4148-9c4a-258afe5b525f X-Archives-Hash: 80f7fb7295d1f8213159f1b9b11cb61e commit: 8f10f75977eefa6285c362170df29351475f1ed7 Author: Anna (cybertailor) Vyalkova sysrq in> AuthorDate: Tue Jan 9 09:02:42 2024 +0000 Commit: Anna Vyalkova sysrq in> CommitDate: Tue Jan 9 09:06:02 2024 +0000 URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=8f10f759 Revert "sci-biology/cmdock: remove unused patches" This reverts commit 1298cd25348ad37dac19c0838415436a8c18d3f5. Signed-off-by: Anna (cybertailor) Vyalkova sysrq.in> sci-biology/cmdock/files/app_info_0.1.4.xml | 40 ++++++++++++++++++++++ .../cmdock/files/cmdock-0.1.4-fix-detection.patch | 15 ++++++++ .../cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml | 15 ++++++++ sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml | 15 ++++++++ 4 files changed, 85 insertions(+) diff --git a/sci-biology/cmdock/files/app_info_0.1.4.xml b/sci-biology/cmdock/files/app_info_0.1.4.xml new file mode 100644 index 0000000000..923a7b9ac1 --- /dev/null +++ b/sci-biology/cmdock/files/app_info_0.1.4.xml @@ -0,0 +1,40 @@ + + + cmdock-boinc-zcp + CurieMarieDock on BOINC + zipped input, checkpoints and progress bar + + + + cmdock-boinc-zcp_wrapper_@PV@ + + + + + + cmdock-boinc-zcp_job_@PV@.xml + + + + docking_out.sd + + + + + cmdock-boinc-zcp + 200 + + cmdock-boinc-zcp_wrapper_@PV@ + + + + cmdock-boinc-zcp_job_@PV@.xml + job.xml + + + + docking_out + docking_out + + + + diff --git a/sci-biology/cmdock/files/cmdock-0.1.4-fix-detection.patch b/sci-biology/cmdock/files/cmdock-0.1.4-fix-detection.patch new file mode 100644 index 0000000000..fceae1e5cf --- /dev/null +++ b/sci-biology/cmdock/files/cmdock-0.1.4-fix-detection.patch @@ -0,0 +1,15 @@ +--- a/meson.build ++++ b/meson.build +@@ -79,8 +79,10 @@ + + cpp_compiler = meson.get_compiler('cpp') + +-extended_encoders_available = (cpp_compiler.has_header('emmintrin.h') and +- host_machine.cpu_family() == 'x86' and host_machine.cpu_family() == 'x86_64') ++extended_encoders_available = ( ++ cpp_compiler.has_header('emmintrin.h') and ++ (host_machine.cpu_family() == 'x86' or host_machine.cpu_family() == 'x86_64') ++) + + if not extended_encoders_available + add_project_arguments('-DBUNDLE_NO_SSE', language: 'cpp') diff --git a/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml new file mode 100644 index 0000000000..074bb29d44 --- /dev/null +++ b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml @@ -0,0 +1,15 @@ + + + @PREFIX@/build/cmdock + docking_log + -c -j 1 -r target.prm -p @PREFIX@/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out + docking_out.chk + docking_out.progress + CMDOCK_ROOT=@PREFIX@ + LD_LIBRARY_PATH=@PREFIX@/build:$LD_LIBRARY_PATH + PERL5LIB=@PREFIX@/lib:$PERL5LIB + + + ligands.zip + + diff --git a/sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml b/sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml new file mode 100644 index 0000000000..a163eb29cf --- /dev/null +++ b/sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml @@ -0,0 +1,15 @@ + + + cmdock + docking_log + -c -j 1 -b 1 -x -r target.prm -p "@PREFIX@/data/scripts/dock.prm" -f htvs.ptc -i ligands.sdf -o docking_out + docking_out.chk + docking_out.progress + CMDOCK_ROOT=@PREFIX@ + LD_LIBRARY_PATH=@PREFIX@/lib:$LD_LIBRARY_PATH + PERL5LIB=@PREFIX@/lib:$PERL5LIB + + + ligands.zip + +