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Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
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QTL
spell-qtl
Commits
06e37325
Commit
06e37325
authored
Jun 02, 2017
by
Damien Leroux
Browse files
Package -AND MANUAL- compile fine so far.
parent
3733e77b
Changes
4
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Inline
Side-by-side
CMakeLists.txt
View file @
06e37325
...
...
@@ -111,22 +111,18 @@ if(${BUILD_FOR_DEPLOYMENT})
add_executable
(
spell-pedigree
${
SPELL_PEDIGREE_SRC
}
${
libstdcpp
}
)
add_executable
(
spell-marker
${
SPELL_MARKER_SRC
}
)
add_executable
(
spell-qtl
${
SPELL_QTL_SRC
}
${
libstdcpp
}
)
add_custom_command
(
OUTPUT glibc.h libstdc++.a COMMAND
${
CMAKE_SOURCE_DIR
}
/deploy/make_old_libc_header.sh WORKING_DIRECTORY
${
CMAKE_BINARY_DIR
}
)
add_custom_command
(
OUTPUT libgmp.a COMMAND
${
CMAKE_SOURCE_DIR
}
/deploy/compile_gmp.sh
${
CMAKE_BINARY_DIR
}
/glibc.h
${
CMAKE_BINARY_DIR
}
WORKING_DIRECTORY
${
CMAKE_SOURCE_DIR
}
/deploy
)
add_custom_command
(
OUTPUT glibc.h libstdc++.a
COMMAND
${
CMAKE_SOURCE_DIR
}
/deploy/make_old_libc_header.sh
WORKING_DIRECTORY
${
CMAKE_BINARY_DIR
}
)
add_custom_command
(
OUTPUT libgmp.a
COMMAND
${
CMAKE_SOURCE_DIR
}
/deploy/compile_gmp.sh
${
CMAKE_BINARY_DIR
}
/glibc.h
${
CMAKE_BINARY_DIR
}
WORKING_DIRECTORY
${
CMAKE_SOURCE_DIR
}
/deploy
)
add_custom_target
(
glibc.h
)
#add_custom_target(stdc++ ${CMAKE_BINARY_DIR}/libstdc++.a)
#add_library(stdc++ INTERFACE IMPORTED)
#set_property(TARGET stdc++ PROPERTY INTERFACE_LINK_LIBRARIES ${CMAKE_BINARY_DIR}/libstdc++.a)
add_library
(
gmp INTERFACE IMPORTED
)
add_custom_target
(
pouet ALL DEPENDS
${
CMAKE_BINARY_DIR
}
/libgmp.a
)
#set_property(TARGET gmp PROPERTY INTERFACE_LINK_LIBRARIES ${CMAKE_BINARY_DIR}/libgmp.a)
#set_target_properties(stdc++ PROPERTIES LINKER_LANGUAGE CXX)
#set_target_properties(gmp PROPERTIES LINKER_LANGUAGE C)
#add_dependencies(gmp stdc++)
#set_source_files_properties(${CMAKE_BINARY_DIR}/libgmp.a PROPERTIES GENERATED TRUE)
#set_source_files_properties(${libstdcpp} PROPERTIES GENERATED TRUE)
#set_source_files_properties(${CMAKE_BINARY_DIR}/libstdc++.a PROPERTIES EXTERNAL_OBJECT TRUE GENERATED TRUE)
SET_SOURCE_FILES_PROPERTIES
(
${
SPELL_PEDIGREE_SRC
}
${
SPELL_MARKER_SRC
}
${
SPELL_QTL_SRC
}
PROPERTIES
...
...
@@ -146,10 +142,6 @@ if(${BUILD_FOR_DEPLOYMENT})
target_link_libraries
(
spell-marker
${
libstdcpp
}
${
CMAKE_BINARY_DIR
}
/libgmp.a
)
target_link_libraries
(
spell-qtl
${
libstdcpp
}
)
target_link_libraries
(
spell-pedigree
${
libstdcpp
}
)
#list(APPEND spell-pedigree_SRC "${CMAKE_BINARY_DIR}/libstdc++.a")
#list(APPEND spell-qtl_SRC "${CMAKE_BINARY_DIR}/libstdc++.a")
#list(APPEND spell-marker_SRC "${CMAKE_BINARY_DIR}/libstdc++.a")
else
()
add_executable
(
spell-pedigree
${
SPELL_PEDIGREE_SRC
}
)
add_executable
(
spell-marker
${
SPELL_MARKER_SRC
}
)
...
...
@@ -183,6 +175,9 @@ add_manpage(spell-marker.1)
add_manpage
(
spell-qtl.1
)
add_manpage
(
spell-qtl-examples.1
)
add_custom_target
(
user_manual.pdf ALL COMMAND ./build_manual.sh
${
CMAKE_BINARY_DIR
}
${
CMAKE_SOURCE_DIR
}
WORKING_DIRECTORY
${
CMAKE_SOURCE_DIR
}
/deploy
)
add_dependencies
(
user_manual.pdf spell-pedigree spell-marker spell-qtl
)
#add_custom_command(OUTPUT spell-marker.1
# COMMAND pandoc -t man ${CMAKE_SOURCE_DIR}/doc/man/spell-marker.1.md -o spell-marker.1
# MAIN_DEPENDENCY ${CMAKE_SOURCE_DIR}/doc/man/spell-marker.1.md
...
...
@@ -202,7 +197,7 @@ add_manpage(spell-qtl-examples.1)
# experimental binaries
#add_executable(test-json sandbox/test-json.cc)
INSTALL
(
TARGETS spell-pedigree spell-marker spell-qtl DESTINATION bin
)
#INSTALL(FILES
...
...
@@ -214,6 +209,9 @@ INSTALL(TARGETS spell-pedigree spell-marker spell-qtl DESTINATION bin)
INSTALL
(
FILES
${
CMAKE_SOURCE_DIR
}
/examples/read-POP.R
DESTINATION share/spell-qtl/examples
)
INSTALL
(
FILES
${
CMAKE_BINARY_DIR
}
/doc/user_manual.pdf
DESTINATION share/doc/spell-qtl
)
INSTALL
(
FILES
${
CMAKE_SOURCE_DIR
}
/examples/three_parents_F2/example1_F2C.gen
${
CMAKE_SOURCE_DIR
}
/examples/three_parents_F2/example1_F2C.phen
...
...
deploy/compile_gmp.sh
View file @
06e37325
...
...
@@ -9,9 +9,11 @@ cd gmp
cd
gmp-6.1.2
||
(
curl https://gmplib.org/download/gmp/gmp-6.1.2.tar.xz
-o
- | xz
-d
|
tar
xf -
&&
cd
gmp-6.1.2
)
# cleanup and configure
[
-f
Makefile
]
&&
make clean
CFLAGS
=
"-include
$PATH_TO_GLIBC_H
"
./configure
--disable-shared
--enable-fake-cpuid
--enable-fat
if
[
-f
Makefile
]
;
then
make clean
else
CFLAGS
=
"-include
$PATH_TO_GLIBC_H
"
./configure
--disable-shared
--enable-fat
fi
# build
make
...
...
doc/user_manual/makefile
View file @
06e37325
...
...
@@ -4,41 +4,51 @@ SRCDIR = /home/sjasson/dev/spel
EXAMPLE_DIR
=
$(SRCDIR)
/examples/three_parents_F2
user_manual.pdf
:
spell-pedigree.tex spell-marker.tex spell-qtl.tex spell-qtl-examples.tex version.tex user_manual.tex images/Spell-pipeline2.svg inputs outputs
user_manual.pdf
:
spell-pedigree.tex spell-marker.tex spell-qtl.tex spell-qtl-examples.tex version.tex user_manual.tex images/Spell-pipeline2.svg inputs outputs
pdflatex
--shell-escape
user_manual.tex
&&
pdflatex
--shell-escape
user_manual.tex
version.tex
:
version.tex
:
git tag |
tail
-1
>
version.tex
spell-pedigree.tex
:
$(SRCDIR)/doc/man/spell-pedigree.1.md
spell-pedigree.tex
:
$(SRCDIR)/doc/man/spell-pedigree.1.md
/usr/bin/pandoc
$(SRCDIR)
/doc/man/spell-pedigree.1.md
--listings
-f
markdown
-t
latex
-o
spell-pedigree.tex
sed
-i
s/
\\
label
\{
/
\l
abel
\{
spell-pedigree:/g spell-pedigree.tex
spell-marker.tex
:
$(SRCDIR)/doc/man/spell-marker.1.md
spell-marker.tex
:
$(SRCDIR)/doc/man/spell-marker.1.md
/usr/bin/pandoc
$(SRCDIR)
/doc/man/spell-marker.1.md
--listings
-f
markdown
-t
latex
-o
spell-marker.tex
sed
-i
s/
\\
label
\{
/
\l
abel
\{
spell-marker:/g spell-marker.tex
spell-qtl.tex
:
../man/spell-qtl.1.md
spell-qtl.tex
:
../man/spell-qtl.1.md
/usr/bin/pandoc
$(SRCDIR)
/doc/man/spell-qtl.1.md
--listings
-f
markdown
-t
latex
-o
spell-qtl.tex
sed
-i
s/
\\
label
\{
/
\l
abel
\{
spell-qtl:/g spell-qtl.tex
spell-qtl-examples.tex
:
$(SRCDIR)/doc/man/spell-qtl-examples.1.md
spell-qtl-examples.tex
:
$(SRCDIR)/doc/man/spell-qtl-examples.1.md
/usr/bin/pandoc
$(SRCDIR)
/doc/man/spell-qtl-examples.1.md
--listings
-f
markdown
-t
latex
-o
spell-qtl-examples.tex
sed
-i
s/
\\
label
\{
/
\l
abel
\{
spell-qtl-examples:/g spell-qtl-examples.tex
inputs
:
input_files/example1.map input_files/example1_F2.phen input_files/example1_F2.gen input_files/example1.ped
:
input_files/%: $(EXAMPLE_DIR)/% input_dir
awk
-v
len
=
73
'{ if (length($$0) > len) print substr($$0, 1, len-3) "..."; else print; }'
$<
>
$@
input_dir
:
mkdir
-p
input_files
awk
-v
len
=
73
'{ if (length($$0) > len) print substr($$0, 1, len-3) "..."; else print; }'
$(EXAMPLE_DIR)
/example1.map
>
input_files/example1.map
awk
-v
len
=
73
'{ if (length($$0) > len) print substr($$0, 1, len-3) "..."; else print; }'
$(EXAMPLE_DIR)
/example1_F2.phen
>
input_files/example1_F2.phen
awk
-v
len
=
73
'{ if (length($$0) > len) print substr($$0, 1, len-3) "..."; else print; }'
$(EXAMPLE_DIR)
/example1_F2.gen
>
input_files/example1_F2.gen
awk
-v
len
=
73
'{ if (length($$0) > len) print substr($$0, 1, len-3) "..."; else print; }'
$(EXAMPLE_DIR)
/example1.ped
>
input_files/example1.ped
inputs
:
input_dir input_files/example1.map input_files/example1_F2.phen input_files/example1_F2.gen input_files/example1.ped
outputs
:
$(BINDIR)
/spell-pedigree
-wd
my_directory
-n
my_name
-p
$(EXAMPLE_DIR)
/example1.ped
my_directory/my_name.spell-pedigree.data
:
$(EXAMPLE_DIR)/example1.ped
$(BINDIR)
/spell-pedigree
-wd
my_directory
-n
my_name
-p
$<
my_directory/my_name.spell-marker.data
:
my_directory/my_name.spell-pedigree.data $(EXAMPLE_DIR)/example1_F2.gen $(EXAMPLE_DIR)/example1_F2C.gen
$(BINDIR)
/spell-marker
-wd
my_directory
-n
my_name
-m
F2:A/B
$(EXAMPLE_DIR)
/example1_F2.gen
-m
F2C:A/C
$(EXAMPLE_DIR)
/example1_F2C.gen
-o
F2,F2C
-O1
-Op
$(BINDIR)
/spell-qtl
-wd
my_directory
-n
my_name
-p
F2
$(EXAMPLE_DIR)
/example1_F2.phen
-p
F2C
$(EXAMPLE_DIR)
/example1_F2C.phen
-gm
$(EXAMPLE_DIR)
/example1.map output-nppop
my_directory/my_name.n-point/ch1/F2/my_name.ch1.F2.0.csv
:
my_directory/my_name.spell-marker.data $(EXAMPLE_DIR)/example1_F2.phen $(EXAMPLE_DIR)/example1_F2C.phen $(EXAMPLE_DIR)/example1.map
$(BINDIR)
/spell-qtl
-wd
my_directory
-n
my_name
-P
auto
-p
F2
$(EXAMPLE_DIR)
/example1_F2.phen
-p
F2C
$(EXAMPLE_DIR)
/example1_F2C.phen
-gm
$(EXAMPLE_DIR)
/example1.map output-nppop
my_directory/my_name.report/t1/t1_report.txt
:
my_directory/my_name.spell-marker.data $(EXAMPLE_DIR)/example1_F2.phen $(EXAMPLE_DIR)/example1_F2C.phen $(EXAMPLE_DIR)/example1.map
$(BINDIR)
/spell-qtl
-wd
my_directory
-n
my_name
-P
auto
-p
F2
$(EXAMPLE_DIR)
/example1_F2.phen
-p
F2C
$(EXAMPLE_DIR)
/example1_F2C.phen
-gm
$(EXAMPLE_DIR)
/example1.map
outputs
:
my_directory/my_name.report/t1/t1_report.txt my_directory/my_name.n-point/ch1/F2/my_name.ch1.F2.0.csv
clean
:
rm
-f
*
.aux
*
.log
*
.pdf
*
.toc
*
.out
*
.lol
...
...
include/computations/frontends4.h
View file @
06e37325
...
...
@@ -2346,6 +2346,11 @@ file& header(file& f, const std::string& str)
inline
/**
* @brief ...
*
* @param mm p_mm:...
*/
void
analysis_report
::
report_final_model
(
model_manager
&
mm
)
{
static
std
::
string
emptystr
;
...
...
@@ -2381,6 +2386,12 @@ void analysis_report::report_final_model(model_manager& mm)
report_file
<<
std
::
string
(
"* There are not enough observations to compute a variance/covariance matrix. Results not displayed."
)
<<
std
::
endl
;
}
else
{
MatrixXd
Pt
=
TM
.
P
.
transpose
();
if
(
Pt
.
size
()
==
0
)
{
Pt
=
MatrixXd
::
Ones
(
1
,
1
);
}
// MSG_DEBUG(TM.P);
// MSG_DEBUG(MATRIX_SIZE(Pt));
// MSG_DEBUG(MATRIX_SIZE(mm.vMcurrent->coefficients()));
MatrixXd
all_coefficients
=
mm
.
vMcurrent
->
coefficients
()
*
Pt
;
/* FIXME use actual full Y instead of un-projecting the traits? */
MatrixXd
all_residuals
=
mm
.
vMcurrent
->
residuals
()
*
Pt
;
...
...
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