--- a/datatypes_conf.xml	Sun Nov 18 17:12:24 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-<datatypes>
-  <datatype_files>
-    <datatype_file name="sra.py"/>
-  </datatype_files>
-  <registration>
-    <datatype extension="sra" type="galaxy.datatypes.binary:Sra" display_in_upload="true"/>
-  </registration>
-  <sniffers>
-    <sniffer type="galaxy.datatypes.binary:Sra"/>
-  </sniffers>
-</datatypes>
\ No newline at end of file

--- a/sra.py	Sun Nov 18 17:12:24 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-"""
-Sra class
-"""
-
-import galaxy.datatypes.binary
-from galaxy.datatypes.binary import Binary
-import data, logging, binascii
-from galaxy.datatypes.metadata import MetadataElement
-from galaxy.datatypes import metadata
-from galaxy.datatypes.sniff import *
-from galaxy import eggs
-import pkg_resources
-pkg_resources.require( "bx-python" )
-import os, subprocess, tempfile
-import struct
-
-class Sra( Binary ):
-    """ Sequence Read Archive (SRA) """
-    file_ext = "sra"
-
-    def __init__( self, **kwd ):
-        Binary.__init__( self, **kwd )
-    def sniff( self, filename ):
-        # The first 8 bytes of any NCBI sra file is 'NCIB.sra', and the file is binary. EBI and DDBJ files may differ. For details
-        # about the format, see http://www.ncbi.nlm.nih.gov/books/n/helpsra/SRA_Overview_BK/#SRA_Overview_BK.4_SRA_Data_Structure
-        try:
-            header = open( filename ).read(8)
-            if binascii.b2a_hex( header ) == binascii.hexlify( 'NCBI.sra' ):
-                return True
-            return False
-        except:
-            return False
-    def set_peek( self, dataset, is_multi_byte=False ):
-        if not dataset.dataset.purged:
-            dataset.peek  = "Binary sra file" 
-            dataset.blurb = data.nice_size( dataset.get_size() )
-        else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
-    def display_peek( self, dataset ):
-        try:
-            return dataset.peek
-        except:
-            return "Binary sra file (%s)" % ( data.nice_size( dataset.get_size() ) )
-
-Binary.register_sniffable_binary_format("sra", "sra", Sra)

--- a/sra_fetch.py	Sun Nov 18 17:12:24 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-from ftplib import FTP
-import sys
-
-# Get accession number from argument
-accession = sys.argv[1]
-outfile = sys.argv[2]
-prefix = accession[0:3]
-middle = accession[3:6]
-suffix = accession[6:9]
-
-# NCBI SRA FTP site
-ftp = FTP('ftp-trace.ncbi.nih.gov')
-
-# Open file and transfer requested SRA as a file
-# Try to change the working directory until it works
-sra = open(outfile, 'wb')
-ftp.login('ftp')
-connected = False
-while not connected:
-    try:
-        ftp.cwd('/sra/sra-instant/reads/ByRun/sra/' + 
-                prefix + '/' +
-                prefix + middle + '/' +
-                prefix + middle + suffix + '/')
-        connected = True
-    except:
-        pass
-        
-ftp.retrbinary('RETR ' + prefix + middle + suffix + '.sra', sra.write)
-ftp.quit()

--- a/sra_fetch.xml	Sun Nov 18 17:12:24 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-<tool id="sra_fetch" name="Fetch SRA" version="1.0.0">
-  <description> by accession from NCBI SRA.</description>
-  <command interpreter="python">sra_fetch.py '$accession' '$output'</command>
-  <inputs>
-    <param name="accession" size="13" type="text" value="SRR000001" label="SRA run accession"/>
-  </inputs>
-  <outputs>
-    <data format="sra" name="output" label="Fetch ${accession.value}"/>
-  </outputs>
-  <requirements>
-    <requirement type="python">sra_fetch.py</requirement>
-  </requirements>
-  <help>
-    This tool fetches SRA archives from NCBI over FTP using the python ftplib.
-  </help>
-</tool>