commit: 8f10f75977eefa6285c362170df29351475f1ed7 Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in> AuthorDate: Tue Jan 9 09:02:42 2024 +0000 Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> 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 <cyber+gentoo <AT> 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 @@ +<app_info> +<app> + <name>cmdock-boinc-zcp</name> + <user_friendly_name>CurieMarieDock on BOINC + zipped input, checkpoints and progress bar</user_friendly_name> +</app> + +<file_info> + <name>cmdock-boinc-zcp_wrapper_@PV@</name> + <sticky/> + <executable/> +</file_info> + +<file_info> + <name>cmdock-boinc-zcp_job_@[email protected]</name> + <sticky/> +</file_info> +<file_info> + <name>docking_out.sd</name> + <sticky/> +</file_info> + +<app_version> + <app_name>cmdock-boinc-zcp</app_name> + <version_num>200</version_num> + <file_ref> + <file_name>cmdock-boinc-zcp_wrapper_@PV@</file_name> + <main_program/> + </file_ref> + <file_ref> + <file_name>cmdock-boinc-zcp_job_@[email protected]</file_name> + <open_name>job.xml</open_name> + <copy_file/> + </file_ref> + <file_ref> + <file_name>docking_out</file_name> + <open_name>docking_out</open_name> + <copy_file/> + </file_ref> +</app_version> +</app_info> 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 @@ +<job_desc> + <task> + <application>@PREFIX@/build/cmdock</application> + <stdout_filename>docking_log</stdout_filename> + <command_line>-c -j 1 -r target.prm -p @PREFIX@/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line> + <checkpoint_filename>docking_out.chk</checkpoint_filename> + <fraction_done_filename>docking_out.progress</fraction_done_filename> + <setenv>CMDOCK_ROOT=@PREFIX@</setenv> + <setenv>LD_LIBRARY_PATH=@PREFIX@/build:$LD_LIBRARY_PATH</setenv> + <setenv>PERL5LIB=@PREFIX@/lib:$PERL5LIB</setenv> + </task> + <unzip_input> + <zipfilename>ligands.zip</zipfilename> + </unzip_input> +</job_desc> 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 @@ +<job_desc> + <task> + <application>cmdock</application> + <stdout_filename>docking_log</stdout_filename> + <command_line>-c -j 1 -b 1 -x -r target.prm -p "@PREFIX@/data/scripts/dock.prm" -f htvs.ptc -i ligands.sdf -o docking_out</command_line> + <checkpoint_filename>docking_out.chk</checkpoint_filename> + <fraction_done_filename>docking_out.progress</fraction_done_filename> + <setenv>CMDOCK_ROOT=@PREFIX@</setenv> + <setenv>LD_LIBRARY_PATH=@PREFIX@/lib:$LD_LIBRARY_PATH</setenv> + <setenv>PERL5LIB=@PREFIX@/lib:$PERL5LIB</setenv> + </task> + <unzip_input> + <zipfilename>ligands.zip</zipfilename> + </unzip_input> +</job_desc>
