Mercurial > repos > mvdbeek > test_sra

annotate README.md @ 10:472f8a7e13b3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
author mvdbeek
date Fri, 14 Aug 2015 13:30:47 -0400
parents ec8b334b5ebb
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
1 [![Build Status](https://travis-ci.org/mdshw5/sra-tools-galaxy.svg?branch=master)](https://travis-ci.org/mdshw5/sra-tools-galaxy)
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
2
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
3 The Galaxy tool wrappers contained in this tool shed repository rely on software developed by
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
4 the NCBI: http://github.com/ncbi/sra-tools.
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
5
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
6 # INSTALLATION
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
7
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
8 Please use the Galaxy admin interface to install from the toolshed: https://toolshed.g2.bx.psu.edu/view/matt-shirley/ncbi_sra_toolkit
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
9
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
10 This software release was designed to install using the Galaxy toolshed under Linux and MacOS operating systems on Intel x86-compatible 32/64 bit architectures.
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
11
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
12 *Build Requirements*
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
13
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
14 - bash
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
15 - git
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
16 - make
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
17 - gcc
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
18 - g++
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
19 - perl
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
20 - libxml2
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
21
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
22 On a Debian OS use:
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
23
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
24 apt-get install build-essential libxml2-dev git
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
25
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
26 On a Mac with [command line tools](https://developer.apple.com/downloads/index.action) installed:
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
27
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
28 brew install git libxml2
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
29
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
30 CONTROLLED-ACCESS DATA
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
31
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
32 Encrypted, controlled-access data is not supported.