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Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
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QTL
spell-qtl
Commits
d7586143
Commit
d7586143
authored
Jun 02, 2017
by
Damien Leroux
Browse files
Manpages: fox a typo. Manual: bits of improvement.
parent
06e37325
Changes
5
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Inline
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doc/man/spell-marker.1.md
View file @
d7586143
...
...
@@ -8,7 +8,7 @@ spell-marker – Compute the 1-point Parental Origin Probabilities in a pedigree
# SYNOPSIS
**spell-marker**
[options...] [
**-
-
wd**
*PATH*
]
**-n**
*NAME*
**-m**
*GEN:FORMAT*
*FILE*
[
**-m**
...]
**spell-marker**
[options...] [
**-wd**
*PATH*
]
**-n**
*NAME*
**-m**
*GEN:FORMAT*
*FILE*
[
**-m**
...]
# DESCRIPTION
...
...
doc/man/spell-pedigree.1.md
View file @
d7586143
...
...
@@ -8,7 +8,7 @@ spell-pedigree – Precompute the Markov Models for a pedigree
# SYNOPSIS
**spell-pedigree**
[
**-h**
] [
**-
-
wd**
*PATH*
]
**-n**
*NAME*
[
**-s**
*CHAR*
]
**-p**
*FILE*
**spell-pedigree**
[
**-h**
] [
**-wd**
*PATH*
]
**-n**
*NAME*
[
**-s**
*CHAR*
]
**-p**
*FILE*
# DESCRIPTION
...
...
doc/man/spell-qtl.1.md
View file @
d7586143
...
...
@@ -8,7 +8,7 @@ spell-qtl – Compute n-point Parental Origin Probabilities and perform QTL anal
# SYNOPSIS
**spell-qtl**
[
*options...*
] [
**-
-
wd**
*PATH*
]
**-n**
*NAME*
**-gm**
*MAP*
**-p**
*GEN*
*TRAITS*
[
**-p**
...] [model and algorithms configuration...]
**spell-qtl**
[
*options...*
] [
**-wd**
*PATH*
]
**-n**
*NAME*
**-gm**
*MAP*
**-p**
*GEN*
*TRAITS*
[
**-p**
...] [model and algorithms configuration...]
# DESCRIPTION
...
...
doc/user_manual/makefile
View file @
d7586143
...
...
@@ -4,8 +4,10 @@ SRCDIR = /home/sjasson/dev/spel
EXAMPLE_DIR
=
$(SRCDIR)
/examples/three_parents_F2
all
:
user_manual.pdf
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
pdflatex
--shell-escape
user_manual.tex
&&
pdflatex
--shell-escape
user_manual.tex
>
/dev/null
version.tex
:
git tag |
tail
-1
>
version.tex
...
...
@@ -13,39 +15,40 @@ version.tex:
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
sed
-i
s/--/-
\{\}
-/g spell-pedigree.tex
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
sed
-i
s/--/-
\{\}
-/g spell-marker.tex
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
sed
-i
s/--/-
\{\}
-/g spell-qtl.tex
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
sed
-i
s/--/-
\{\}
-/g spell-qtl-examples.tex
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
:
input_files/example1.map input_files/example1_F2.phen input_files/example1_F2.gen input_files/example1.ped
:
input_files/%: $(EXAMPLE_DIR)/%
mkdir
-p
input_files
awk
-v
len
=
69
'{ if (length($$0) > len) print substr($$0, 1, len-3) "..."; else print; }'
$<
>
$@
inputs
:
input_dir
input_files/example1.map input_files/example1_F2.phen input_files/example1_F2.gen input_files/example1.ped
inputs
:
input_files/example1.map input_files/example1_F2.phen input_files/example1_F2.gen input_files/example1.ped
my_directory/my_name.spell-pedigree.data
:
$(EXAMPLE_DIR)/example1.ped
my_directory/my_name.
cache/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
my_directory/my_name.
cache/my_name.
spell-marker.data
:
my_directory/my_name.
cache/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
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
my_directory/my_name.n-point/ch1/F2/my_name.ch1.F2.0.csv
:
my_directory/my_name.
cache/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
my_directory/my_name.report/t1/t1_report.txt
:
my_directory/my_name.
cache/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
...
...
doc/user_manual/user_manual.tex
View file @
d7586143
...
...
@@ -19,7 +19,8 @@
\lstset
{
breakatwhitespace=false,
breaklines=true
breaklines=true,
basicstyle=
\ttfamily
}
...
...
@@ -28,20 +29,20 @@ breaklines=true
\setlength
{
\itemsep
}{
0pt
}
\setlength
{
\parskip
}{
0pt
}}
\newcommand\myfolder
[2][white]
{
%
\begin{tikzpicture}
[overlay]
\begin{scope}
[xshift=20pt]
\filldraw
[rounded corners=1pt,fill=#1,draw=white,double=black]
(-23pt,10pt) -- ++(3pt,5pt) -- ++(18pt,0pt) -- ++(40:3pt) -- ++(9pt,0pt) -- ++(-40:3pt)
-- (20pt,15pt) -- (23pt,10pt) -- cycle;
\filldraw
[rounded corners,draw=white,double=black,top color=#1,bottom color=#1!30]
(-22pt,-12pt) -- ++(44pt,0pt) -- (25pt,12pt) coordinate (topr) -- ++(-50pt,0pt) coordinate (topl) -- cycle;
\end{scope}
\end{tikzpicture}
%
\makebox
[35pt]
{
\raisebox
{
-3pt
}{{
\ttfamily
/#2
}}}
%
}
%
%
\newcommand\myfolder[2][white]{%
%
\begin{tikzpicture}[overlay]
%
\begin{scope}[xshift=20pt]
%
\filldraw[rounded corners=1pt,fill=#1,draw=white,double=black]
%
(-23pt,10pt) -- ++(3pt,5pt) -- ++(18pt,0pt) -- ++(40:3pt) -- ++(9pt,0pt) -- ++(-40:3pt)
%
-- (20pt,15pt) -- (23pt,10pt) -- cycle;
%
\filldraw[rounded corners,draw=white,double=black,top color=#1,bottom color=#1!30]
%
(-22pt,-12pt) -- ++(44pt,0pt) -- (25pt,12pt) coordinate (topr) -- ++(-50pt,0pt) coordinate (topl) -- cycle;
%
\end{scope}
%
\end{tikzpicture}%
%
\makebox[35pt]{\raisebox{-3pt}{{\ttfamily/#2}}}%
%
}
%
...
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