argument fasta

Merk.txt

+Verzeichnisstruktur beim prepare 
+    dbname+_+tool. keine unterverzeichnisse: skripte wäre komplizierter. man müsste in jedem verzechnis gehen bei 
+    operationen und wieder rauskommen

blast_db.sh

@@ -6,5 +6,4 @@ TOOL_FILE=$2
 
 cd $TOOL_DIR
 makeblastdb -dbtype prot -in $TOOL_FILE
-rm $TOOL_FILE
 cd -
\ No newline at end of file

delete_db.sh

 #!/bin/bash
 
-database=$1
-file=$2
-cd $file
-rm $database*
-cd -
\ No newline at end of file
+WEB_FILE=$1
+s3cmd del $WEB_FILE 
\ No newline at end of file

download_db.sh

 #!/bin/bash
-Target_file=$1
-Target_dir=$2
-
-s3cmd get $Target_file $Target_dir
+TARGET_FILE=$1
+TARGET_DIR=$2
+FILE_NAME=$3
+cd $TARGET_DIR
+s3cmd get $TARGET_FILE 
+tar -xzvf $FILE_NAME
+rm $FILE_NAME
+cd -
\ No newline at end of file

ghostx_db.sh

@@ -4,5 +4,4 @@ TOOL_DIR=$1
 TOOL_FILE=$2
 cd $TOOL_DIR
 ghostx db -i $TOOL_FILE -o ghostx_db
-rm $TOOL_FILE
 cd -
\ No newline at end of file

hmmer_pfam.sh

 #!/bin/bash
+TOOL_DIR=$1
+TOOL_FILE=$2
+
+
+cd $TOOL_DIR
+hmmpress $TOOL_FILE
+cd -
\ No newline at end of file

prepare_card.sh

@@ -4,4 +4,5 @@ DOWNLOAD_DIR=$1
 cd $DOWNLOAD_DIR
 wget https://card.mcmaster.ca/download/0/broadstreet-v3.0.3.tar.gz
 tar xjf broadstreet-v3.0.3.tar.gz
+rm broadstreet-v3.0.3.tar.gz
 cd -
\ No newline at end of file

testfile.txt

@@ -92,4 +92,5 @@ Database repository---> https://github.com/MGX-metagenomics/databases/blob/maste
 
 anzeigen lassen---> echo $VARIABLE
 löschen---> unset VARIABLE
-setzen---> export VARIABLE = pfad
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+setzen---> export VARIABLE = pfad
+

upload_db.sh

 #!/bin/bash
-DATA_DB=$1
-TARGET_FILE=$2
+DATA_DIR=$1
+TARGET_DIR_NAME=$2
 TARGET_DIR=$3
-TARGET_FILE_NAME=$4
-cd $DATA_DB
-tar -czvf $TARGET_FILE_NAME $TARGET_FILE
-s3cmd put $TARGET_FILE_NAME $TARGET_DIR
-rm $TARGET_FILE_NAME
+UPLOAD_DIR=$4
+cd $DATA_DIR
+tar -czvf $TARGET_DIR_NAME $TARGET_DIR
+s3cmd put $TARGET_DIR_NAME $UPLOAD_DIR
+rm $TARGET_DIR_NAME
 cd -
\ No newline at end of file