Commit da57157a authored by Rudel Fankep's avatar Rudel Fankep
Browse files

programm run

parent e6f821cc
Verzeichnisstruktur beim prepare
dbname+_+tool. keine unterverzeichnisse: skripte wäre komplizierter. man müsste in jedem verzechnis gehen bei
operationen und wieder rauskommen
#!/bin/bash
TOOL_DIR=$1
TOOL_DIRECTORY=$1
TOOL_FILE=$2
cd $TOOL_DIR
cd $TOOL_DIRECTORY
makeblastdb -dbtype prot -in $TOOL_FILE
cd -
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#!/bin/bash
WEB_FILE=$1
s3cmd del $WEB_FILE
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#!/bin/bash
REMOTE_FILE=$1
s3cmd del $REMOTE_FILE
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#!/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 -
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#!/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 -
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#!/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 -
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#!/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 -
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#!/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 -
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#!/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 -
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#!/usr/bin/env python
import pkg_resources
print(pkg_resources.resource_filename(__name__, "blast_db.sh"))
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
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#!/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 -
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