Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Aflitos, Saulo Alves
mapper
Commits
9b2ca054
Commit
9b2ca054
authored
Apr 26, 2013
by
Aflitos, Saulo Alves
Browse files
bug fix
parent
c4347ffc
Changes
6
Expand all
Hide whitespace changes
Inline
Side-by-side
.gitignore
View file @
9b2ca054
...
...
@@ -6,3 +6,4 @@
*.dot
*.png
*.html
*.out
SConstruct.run
View file @
9b2ca054
#!/bin/bash
set
-xeu
LOGFILE
=
"SConstruct.run.log."
`
date
+%Y%m%d_%H%M%S
`
".out"
#echo "LOGFILE $LOGFILE"
python scons/scons.py
-n
--stack-size
=
1024
--diskcheck
=
none
$@
2>&1 |
tee
$LOGFILE
SConstruct.tree.sh
View file @
9b2ca054
...
...
@@ -4,7 +4,7 @@ rm SConstruct.tree.png 2>/dev/null
rm
SConstruct.tree.gif 2>/dev/null
rm
SConstruct.tree.html 2>/dev/null
bash SConstruct.run
-n
--tree
=
prune,status
$@
>
SConstruct.tree.dat
bash SConstruct.run
-n
--tree
=
prune,status
$@
|
grep
-v
'+-/'
>
SConstruct.tree.dat
#,derived
cat
SConstruct.tree.dat | python SConstruct.graph.py
$@
...
...
all.csv
0 → 100644
View file @
9b2ca054
#in fasta in csv
sa1/sa.fa sa1/sa.csv
#sa2/sa.fa sa2/sa.csv
sh1/sh.fa sh1/sh.csv
#sh2/sh.fa sh2/sh.csv
#sl1/sl.fa sl1/sl.csv
#sl2/sl.fa sl2/sl.csv
sp1/sp.fa sp1/sp.csv
#sp2/sp.fa sp2/sp.csv
run2.py
View file @
9b2ca054
This diff is collapsed.
Click to expand it.
sp1/sp.csv
View file @
9b2ca054
#group name platform library name library size library size min library size max file names
1205
1
2_I238_FC
C0U42
ACXX_L
1
_SZAXPI00
8753-79
illumina pe
500 450 550
/home/assembly/tomato150/
reseq/raw/074
/illumina/pairedend_
50
0/1205
1
2_I238_FC
C0U42
ACXX_L
1
_SZAXPI00
8753-79_1
.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/
reseq/raw/074
/illumina/pairedend_
50
0/1205
1
2_I238_FC
C0U42
ACXX_L
1
_SZAXPI00
8753-79_2
.fq.gz.clean.dup.clean.gz
1205
24
_I23
8
_FC
D1174
ACXX_L4_SZAXPI009266-140 illumina pe 170 153 187 /home/assembly/tomato150/denovo/pennellii/
raw
/illumina/pairedend_170/1205
24
_I23
8
_FC
D1174
ACXX_L4_SZAXPI009266-140_
2
.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
raw
/illumina/pairedend_170/1205
24
_I23
8
_FC
D1174
ACXX_L4_SZAXPI009266-140_
1
.fq.gz.clean.dup.clean.gz
120530_I235_FC
C0U06
ACXX_L
4
_SZAXPI009266-140 illumina pe 170 153 187 /home/assembly/tomato150/denovo/pennellii/
raw
/illumina/pairedend_170/120530_I235_FC
C0U06
ACXX_L
4
_SZAXPI009266-140_
1
.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
raw
/illumina/pairedend_170/120530_I235_FC
C0U06
ACXX_L
4
_SZAXPI009266-140_
2
.fq.gz.clean.dup.clean.gz
1205
30
_I23
5
_FC
D117Y
ACXX_L1_SZAXPI00
9266-140
illumina pe
170 153 187
/home/assembly/tomato150/
denovo/pennellii/raw
/illumina/pairedend_
17
0/1205
30
_I23
5
_FC
D117Y
ACXX_L1_SZAXPI00
9266-140_2
.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/
denovo/pennellii/raw
/illumina/pairedend_
17
0/1205
30
_I23
5
_FC
D117Y
ACXX_L1_SZAXPI00
9266-140_1
.fq.gz.clean.dup.clean.gz
120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/
raw
/illumina/matepair_2000/120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
raw
/illumina/matepair_2000/120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/
raw
/illumina/matepair_2000/120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
raw
/illumina/matepair_2000/120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz
120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/
raw
/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
raw
/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz
120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/
raw
/illumina/matepair_2000/120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
raw
/illumina/matepair_2000/120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/
raw
/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
raw
/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
20000.dedup
454 mp
20000
18000
22000
/home/assembly/tomato150/denovo/pennellii/filtered/454/20000/20000.dedup.sff
8000.dedup
454 mp 8000 7200 8800
/home/assembly/tomato150/denovo/pennellii/filtered/454/8000/8000.dedup.sff
12052
4
_I238_FC
D1174
ACXX_L
4
_SZAXPI00
9266-140
illumina pe
170 153 187
/home/assembly/tomato150/
denovo/pennellii/filtered
/illumina/pairedend_
17
0/12052
4
_I238_FC
D1174
ACXX_L
4
_SZAXPI00
9266-140_2
.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/
denovo/pennellii/filtered
/illumina/pairedend_
17
0/12052
4
_I238_FC
D1174
ACXX_L
4
_SZAXPI00
9266-140_1
.fq.gz.clean.dup.clean.gz
1205
30
_I23
5
_FC
C0U06
ACXX_L4_SZAXPI009266-140 illumina pe 170 153 187 /home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/pairedend_170/1205
30
_I23
5
_FC
C0U06
ACXX_L4_SZAXPI009266-140_
1
.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/pairedend_170/1205
30
_I23
5
_FC
C0U06
ACXX_L4_SZAXPI009266-140_
2
.fq.gz.clean.dup.clean.gz
120530_I235_FC
D117Y
ACXX_L
1
_SZAXPI009266-140 illumina pe 170 153 187 /home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/pairedend_170/120530_I235_FC
D117Y
ACXX_L
1
_SZAXPI009266-140_
2
.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/pairedend_170/120530_I235_FC
D117Y
ACXX_L
1
_SZAXPI009266-140_
1
.fq.gz.clean.dup.clean.gz
1205
12
_I23
8
_FC
C0U42
ACXX_L1_SZAXPI00
8753-79
illumina pe
500 450 550
/home/assembly/tomato150/
reseq/filtered/074
/illumina/pairedend_
50
0/1205
12
_I23
8
_FC
C0U42
ACXX_L1_SZAXPI00
8753-79_1
.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/
reseq/filtered/074
/illumina/pairedend_
50
0/1205
12
_I23
8
_FC
C0U42
ACXX_L1_SZAXPI00
8753-79_2
.fq.gz.clean.dup.clean.gz
120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/matepair_2000/120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/matepair_2000/120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/matepair_2000/120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/matepair_2000/120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz
120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz
120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/matepair_2000/120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/matepair_2000/120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
20000.dedup
454 mp
20000
18000
22000
/home/assembly/tomato150/denovo/pennellii/filtered/454/20000/20000.dedup.sff
8000.dedup
454 mp 8000 7200 8800
/home/assembly/tomato150/denovo/pennellii/filtered/454/8000/8000.dedup.sff
3000.dedup 454 mp 3000 2700 3300 /home/assembly/tomato150/denovo/pennellii/filtered/454/3000/3000.dedup.sff
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment
