* [gentoo-commits] repo/proj/guru:master commit in: sci-biology/cmdock/files/
@ 2021-05-21 14:10 Michał Górny
0 siblings, 0 replies; 4+ messages in thread
From: Michał Górny @ 2021-05-21 14:10 UTC (permalink / raw
To: gentoo-commits
commit: 08de1b6acdc9e1957c4b1690d683818d7fb6841c
Author: Anna Vyalkova <cyber <AT> sysrq <DOT> in>
AuthorDate: Thu May 20 21:48:57 2021 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Thu May 20 21:48:57 2021 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=08de1b6a
sci-biology/cmdock/files: fix filenames
Signed-off-by: Anna Vyalkova <cyber <AT> sysrq.in>
sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml | 2 +-
sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
index 3b89cdfd2..2691d09ea 100644
--- a/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
+++ b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
@@ -1,6 +1,6 @@
<job_desc>
<task>
- <application>/opt/cmdock/build/cmdock-0.1.2</application>
+ <application>/opt/cmdock-0.1.2/build/cmdock</application>
<stdout_filename>docking_log</stdout_filename>
<command_line>-r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
<setenv>CMDOCK_ROOT=/opt/cmdock-0.1.2</setenv>
diff --git a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml
index aa3042498..c670b677e 100644
--- a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml
+++ b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml
@@ -1,6 +1,6 @@
<job_desc>
<task>
- <application>/opt/cmdock/build/cmdock-0.1.2</application>
+ <application>/opt/cmdock-0.1.2/build/cmdock</application>
<stdout_filename>docking_log</stdout_filename>
<command_line>-r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
<setenv>CMDOCK_ROOT=/opt/cmdock-0.1.2</setenv>
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] repo/proj/guru:master commit in: sci-biology/cmdock/files/
@ 2021-05-22 18:45 Andrew Ammerlaan
0 siblings, 0 replies; 4+ messages in thread
From: Andrew Ammerlaan @ 2021-05-22 18:45 UTC (permalink / raw
To: gentoo-commits
commit: 832e0124b98de06cdd097aefa69b81aec8f97191
Author: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Fri May 21 07:15:58 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sat May 22 15:21:07 2021 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=832e0124
sci-biology/cmdock/files: increment <version_num/>
Signed-off-by: Anna Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/files/app_info.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/cmdock/files/app_info.xml b/sci-biology/cmdock/files/app_info.xml
index 6a41b0bb2..eb222052b 100644
--- a/sci-biology/cmdock/files/app_info.xml
+++ b/sci-biology/cmdock/files/app_info.xml
@@ -47,7 +47,7 @@
</app_version>
<app_version>
<app_name>cmdock-boinc-zip</app_name>
- <version_num>100</version_num>
+ <version_num>200</version_num>
<file_ref>
<file_name>cmdock-boinc-zip_wrapper_0.1.2</file_name>
<main_program/>
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] repo/proj/guru:master commit in: sci-biology/cmdock/files/
@ 2023-12-31 15:28 David Roman
0 siblings, 0 replies; 4+ messages in thread
From: David Roman @ 2023-12-31 15:28 UTC (permalink / raw
To: gentoo-commits
commit: 1298cd25348ad37dac19c0838415436a8c18d3f5
Author: Michael Mair-Keimberger <mmk <AT> levelnine <DOT> at>
AuthorDate: Sat Dec 30 18:16:39 2023 +0000
Commit: David Roman <davidroman96 <AT> gmail <DOT> com>
CommitDate: Sat Dec 30 18:20:01 2023 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=1298cd25
sci-biology/cmdock: remove unused patches
Signed-off-by: Michael Mair-Keimberger <mmk <AT> levelnine.at>
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 deletions(-)
diff --git a/sci-biology/cmdock/files/app_info_0.1.4.xml b/sci-biology/cmdock/files/app_info_0.1.4.xml
deleted file mode 100644
index 923a7b9ac1..0000000000
--- a/sci-biology/cmdock/files/app_info_0.1.4.xml
+++ /dev/null
@@ -1,40 +0,0 @@
-<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_@PV@.xml</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_@PV@.xml</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
deleted file mode 100644
index fceae1e5cf..0000000000
--- a/sci-biology/cmdock/files/cmdock-0.1.4-fix-detection.patch
+++ /dev/null
@@ -1,15 +0,0 @@
---- 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
deleted file mode 100644
index 074bb29d44..0000000000
--- a/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<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
deleted file mode 100644
index a163eb29cf..0000000000
--- a/sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<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>
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] repo/proj/guru:master commit in: sci-biology/cmdock/files/
@ 2024-01-09 12:03 David Roman
0 siblings, 0 replies; 4+ messages in thread
From: David Roman @ 2024-01-09 12:03 UTC (permalink / raw
To: gentoo-commits
commit: 8f10f75977eefa6285c362170df29351475f1ed7
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Tue Jan 9 09:02:42 2024 +0000
Commit: David Roman <davidroman96 <AT> gmail <DOT> com>
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_@PV@.xml</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_@PV@.xml</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>
^ permalink raw reply related [flat|nested] 4+ messages in thread
end of thread, other threads:[~2024-01-09 12:03 UTC | newest]
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2021-05-21 14:10 [gentoo-commits] repo/proj/guru:master commit in: sci-biology/cmdock/files/ Michał Górny
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2021-05-22 18:45 Andrew Ammerlaan
2023-12-31 15:28 David Roman
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