Mercurial > repos > mingchen0919 > statonlab_interprocan

comparison interproscan.Rmd @ 2:3e4a0719caa7 draft

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update
author mingchen0919
date Tue, 03 Apr 2018 15:06:55 -0400
parents 035457a30aea
children 10acf59ba351
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1:035457a30aea 2:3e4a0719caa7
12 12
13 13
14 # InterProScan job script 14 # InterProScan job script
15 15
16 ```{bash echo=FALSE} 16 ```{bash echo=FALSE}
17 # create two directorys: tempdir and output-dir
18 mkdir -p ${X_d}/temp_dir
19 mkdir -p ${X_d}/output_dir
20
17 #---- build job script ---- 21 #---- build job script ----
18 cat >temp.sh <<EOL 22 cat >temp.sh <<EOL
19 /opt/main/InterProScan/5.28-67.0/interproscan.sh \\ 23 /opt/main/InterProScan/5.28-67.0/interproscan.sh \\
20 -i ${X_A} \\ 24 -i ${X_A} \\
21 -f ${X_B} \\ 25 -f ${X_B} \\
22 --disable-precalc ${X_C} \\ 26 --disable-precalc ${X_C} \\
23 --iprlookup ${X_D} \\ 27 --iprlookup ${X_D} \\
24 --goterms ${X_E} \\ 28 --goterms ${X_E} \\
25 --pathways ${X_F} \\ 29 --pathways ${X_F} \\
26 --tempdir ${X_D}/temp_dir \\ 30 --tempdir ${X_d}/temp_dir \\
27 --output-dir ${X_D}/output_dir > /dev/null 2>&1 31 --output-dir ${X_d}/output_dir > /dev/null 2>&1
28 32
29 EOL 33 EOL
30 34
31 # remove empty input lines 35 # remove empty input lines
32 grep -v 'None' temp.sh |\ 36 grep -v 'None' temp.sh |\