malacology/RGBEPP
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polish: make the Directory can also be changed

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kuoi 2024-12-09 16:51:23 +11:00
parent c91b0f8fb2
commit bbc3d7fe82
2 changed files with 21 additions and 2 deletions
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14
RGBEPP.d
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@ -581,8 +581,8 @@ void main(string[] args) {
string DirHome = std.file.getcwd(); string DirHome = std.file.getcwd();
string DirRaw = buildPath(DirHome, "00_raw"); string DirRaw = buildPath(DirHome, "00_raw");
string DirQcTrim = buildPath(DirHome, "01_fastp"); string DirQcTrim = buildPath(DirHome, "01_fastp");
string DirMap = buildPath(DirHome, "02_bowtie2"); string DirAssembly = buildPath(DirHome, "02_spades");
string DirAssembly = buildPath(DirHome, "03_spades"); string DirMap = buildPath(DirHome, "03_bowtie2");
string DirBam = buildPath(DirHome, "04_bam"); string DirBam = buildPath(DirHome, "04_bam");
string DirVcf = buildPath(DirHome, "05_vcf"); string DirVcf = buildPath(DirHome, "05_vcf");
string DirConsensus = buildPath(DirHome, "06_consen"); string DirConsensus = buildPath(DirHome, "06_consen");
@ -716,6 +716,16 @@ void main(string[] args) {
PathDelstop = getValueFromConfig(ARG_C, "delstop"); PathDelstop = getValueFromConfig(ARG_C, "delstop");
PathTrimal = getValueFromConfig(ARG_C, "trimal"); PathTrimal = getValueFromConfig(ARG_C, "trimal");
DirRaw = getValueFromConfig(ARG_C, "raw_dir");
DirQcTrim = getValueFromConfig(ARG_C, "fastp_dir");
DirAssembly = getValueFromConfig(ARG_C, "spades_dir");
DirMap = getValueFromConfig(ARG_C, "bowtie2_dir");
DirBam = getValueFromConfig(ARG_C, "bam_dir");
DirVcf = getValueFromConfig(ARG_C, "vcf_dir");
DirConsensus = getValueFromConfig(ARG_C, "consen_dir");
DirAlign = getValueFromConfig(ARG_C, "macse_dir");
DirTrim = getValueFromConfig(ARG_C, "trimal_dir");
} }
writeln("RGBEPP::Start"); writeln("RGBEPP::Start");

9
config.example
View file

@ -9,3 +9,12 @@ exonerate = /usr/bin/exonerate
macse = /usr/share/java/macse.jar macse = /usr/share/java/macse.jar
delstop = /usr/bin/delstop delstop = /usr/bin/delstop
trimal = /usr/bin/trimal trimal = /usr/bin/trimal
raw_dir = 00_raw
fastp_dir = 01_fastp
spades_dir = 02_spades
bowtie2_dir = 03_bowtie2
bam_dir = 04_bam
vcf_dir = 05_vcf
consen_dir = 06_consen
macse_dir = 07_macse
trimal_dir = 08_trimal