Commit e6f821cc authored by Rudel Fankep's avatar Rudel Fankep
Browse files

argument fasta

parent dd9ddf79
Verzeichnisstruktur beim prepare
dbname+_+tool. keine unterverzeichnisse: skripte wäre komplizierter. man müsste in jedem verzechnis gehen bei
operationen und wieder rauskommen
...@@ -6,5 +6,4 @@ TOOL_FILE=$2 ...@@ -6,5 +6,4 @@ TOOL_FILE=$2
cd $TOOL_DIR cd $TOOL_DIR
makeblastdb -dbtype prot -in $TOOL_FILE makeblastdb -dbtype prot -in $TOOL_FILE
rm $TOOL_FILE
cd - cd -
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#!/bin/bash #!/bin/bash
database=$1 WEB_FILE=$1
file=$2 s3cmd del $WEB_FILE
cd $file \ No newline at end of file
rm $database*
cd -
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#!/bin/bash #!/bin/bash
Target_file=$1 TARGET_FILE=$1
Target_dir=$2 TARGET_DIR=$2
FILE_NAME=$3
s3cmd get $Target_file $Target_dir cd $TARGET_DIR
s3cmd get $TARGET_FILE
tar -xzvf $FILE_NAME
rm $FILE_NAME
cd -
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...@@ -4,5 +4,4 @@ TOOL_DIR=$1 ...@@ -4,5 +4,4 @@ TOOL_DIR=$1
TOOL_FILE=$2 TOOL_FILE=$2
cd $TOOL_DIR cd $TOOL_DIR
ghostx db -i $TOOL_FILE -o ghostx_db ghostx db -i $TOOL_FILE -o ghostx_db
rm $TOOL_FILE
cd - cd -
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#!/bin/bash #!/bin/bash
TOOL_DIR=$1
TOOL_FILE=$2
cd $TOOL_DIR
hmmpress $TOOL_FILE
cd -
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...@@ -4,4 +4,5 @@ DOWNLOAD_DIR=$1 ...@@ -4,4 +4,5 @@ DOWNLOAD_DIR=$1
cd $DOWNLOAD_DIR cd $DOWNLOAD_DIR
wget https://card.mcmaster.ca/download/0/broadstreet-v3.0.3.tar.gz wget https://card.mcmaster.ca/download/0/broadstreet-v3.0.3.tar.gz
tar xjf broadstreet-v3.0.3.tar.gz tar xjf broadstreet-v3.0.3.tar.gz
rm broadstreet-v3.0.3.tar.gz
cd - cd -
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...@@ -92,4 +92,5 @@ Database repository---> https://github.com/MGX-metagenomics/databases/blob/maste ...@@ -92,4 +92,5 @@ Database repository---> https://github.com/MGX-metagenomics/databases/blob/maste
anzeigen lassen---> echo $VARIABLE anzeigen lassen---> echo $VARIABLE
löschen---> unset VARIABLE löschen---> unset VARIABLE
setzen---> export VARIABLE = pfad setzen---> export VARIABLE = pfad
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#!/bin/bash #!/bin/bash
DATA_DB=$1 DATA_DIR=$1
TARGET_FILE=$2 TARGET_DIR_NAME=$2
TARGET_DIR=$3 TARGET_DIR=$3
TARGET_FILE_NAME=$4 UPLOAD_DIR=$4
cd $DATA_DB cd $DATA_DIR
tar -czvf $TARGET_FILE_NAME $TARGET_FILE tar -czvf $TARGET_DIR_NAME $TARGET_DIR
s3cmd put $TARGET_FILE_NAME $TARGET_DIR s3cmd put $TARGET_DIR_NAME $UPLOAD_DIR
rm $TARGET_FILE_NAME rm $TARGET_DIR_NAME
cd - cd -
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