programm run

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

 #!/bin/bash
 
-TOOL_DIR=$1
+TOOL_DIRECTORY=$1
 TOOL_FILE=$2
 
 
-cd $TOOL_DIR
+cd $TOOL_DIRECTORY
 makeblastdb -dbtype prot -in $TOOL_FILE
 cd -
\ No newline at end of file

delete_db.sh

-#!/bin/bash
-
-WEB_FILE=$1
-s3cmd del $WEB_FILE 
\ No newline at end of file

delete_remote_file.sh

+#!/bin/bash
+
+REMOTE_FILE=$1
+s3cmd del $REMOTE_FILE 
\ No newline at end of file

download_db.sh

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

ghostx_db.sh

 #!/bin/bash
 
-TOOL_DIR=$1
-TOOL_FILE=$2
-cd $TOOL_DIR
-ghostx db -i $TOOL_FILE -o ghostx_db
+TOOL_DIRECTORY=$1
+RAW_FILE=$2
+cd $TOOL_DIRECTORY
+ghostx db -i $RAW_FILE -o ghostx_db
 cd -
\ No newline at end of file

hmmer_pfam.sh

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

local_databases/dbman_metadata.json

+[]
\ No newline at end of file

prepare_card.sh

 #!/bin/bash
-DOWNLOAD_DIR=$1
+LOCAL_DATABASE_DIRECTORY=$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 $LOCAL_DATABASE_DIRECTORY
+wget --content-disposition https://card.mcmaster.ca/latest/data
+tar xfa card-data.tar.bz2
+rm card-data.tar.bz2
 cd -
\ No newline at end of file

prepare_pfam.sh

 #!/bin/bash
-DOWNLOAD_DIR=$1
+LOCAL_DATABASE_DIRECTORY=$1
 
-cd $DOWNLOAD_DIR
+cd $LOCAL_DATABASE_DIRECTORY
 wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz
 gunzip Pfam-A.hmm.gz
 cd -
\ No newline at end of file

prepare_swissprot.sh

 #!/bin/bash
-DOWNLOAD_DIR=$1
+LOCAL_DATABASE_DIRECTORY=$1
 
-cd $DOWNLOAD_DIR
+cd $LOCAL_DATABASE_DIRECTORY
 wget ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/uniprot_sprot.fasta.gz
 gunzip uniprot_sprot.fasta.gz
 cd -
\ No newline at end of file

test.py

+#!/usr/bin/env python
+import pkg_resources
+
+print(pkg_resources.resource_filename(__name__, "blast_db.sh"))

testfile.txt

-
 Dbxref Quellcode, evtl. als Vorlage nutzbar: https://git.computational.bio.uni-giessen.de/SOaAS/dbxref/tree/master/dbxref
 
 Beschreibung:
@@ -36,16 +35,8 @@ Beispieldatenbanken:
 
 Evtl. kann auch biomaj für das Problem genutzt werden: https://biomaj.genouest.org/
 
-#####sudo apt-get install ncbi-blast+######
-
-
 Beispielaufrufe: 
 
-
-
-upload only name write. ort soll bekannt sein
-entpacken beim download (tar xzf)
-	
 	# Vorher: In dem Datenbankverzeichnis liegt keine swiss-prot Datenbank fuer ghostx
 	dbman prepare "UniprotKB/swiss-prot" "ghostx"
 	-> Ergebnis: In dem Datenbankvorbereitungsverzeichnis liegt die ghostx Datenbank. die datenbank kann benutzt werden
@@ -82,15 +73,14 @@ entpacken beim download (tar xzf)
                 pfam[hmmer] version: x.y.z erstellt am: <datum>
 
 
-default='s3://db_storage'
-
-
-
-ordner mit entsprechende namen!!!!
-
 Database repository---> https://github.com/MGX-metagenomics/databases/blob/master/card.build 
 
 anzeigen lassen---> echo $VARIABLE
 löschen---> unset VARIABLE
 setzen---> export VARIABLE = pfad
 
+https://setuptools.readthedocs.io/en/latest/pkg_resources.html#basic-resource-access
+
+-->ResourceManager API¶
+
+https://docs.python.org/3.7/library/tempfile.html
\ No newline at end of file

upload_db.sh

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