updates s3cmd so uploads won't be missing

README.md

@@ -6,7 +6,7 @@ is software for RNA-seq analysis.
 
 **the website.**
 
-### [Download](https://github.com/nellore/rail/raw/v0.2.3a/releases/install_rail-rna-0.2.3a)
+### [Download](https://github.com/nellore/rail/raw/v0.2.3b/releases/install_rail-rna-0.2.3b)
 
 **the latest stable release. Read the**
 
@@ -37,7 +37,7 @@ Outputs currently include
 
 and will likely expand in future versions.
 
-Read the [preprint](http://biorxiv.org/content/early/2015/08/11/019067) for more details. Methods explained there correspond to Rail-RNA 0.2.3a.
+Read the [preprint](http://biorxiv.org/content/early/2015/08/11/019067) for more details. Methods explained there correspond to Rail-RNA 0.2.3b.
 
 Get set up
 -----
@@ -47,17 +47,17 @@ Start with a recent (>= 2009) OS X or Linux box. For a no-fuss install, enter
 curl http://verve.webfactional.com/rail -o $INSTALLER; python2 $INSTALLER -m || true;
 rm -f $INSTALLER)
 ```
-at a Bash prompt. For a more customizable install, download [`install_rail-rna-0.2.3a`](https://github.com/nellore/rail/raw/v0.2.3a/releases/install_rail-rna-0.2.3a), change to the directory containing it, and make the installer executable with
+at a Bash prompt. For a more customizable install, download [`install_rail-rna-0.2.3b`](https://github.com/nellore/rail/raw/v0.2.3b/releases/install_rail-rna-0.2.3b), change to the directory containing it, and make the installer executable with
 ```
-chmod +x install_rail-rna-0.2.3a
+chmod +x install_rail-rna-0.2.3b
 ```
 Now run
 ```
-sudo ./install_rail-rna-0.2.3a
+sudo ./install_rail-rna-0.2.3b
 ```
 to install for all users or
 ```
-./install_rail-rna-0.2.3a
+./install_rail-rna-0.2.3b
 ```
 to install for just you. Refer to [these](http://docs.rail.bio/installation/) detailed installation instructions from the [docs](http://docs.rail.bio) for more information. If the executable doesn't work, you may need [Python](http://www.python.org). You'll also need Bowtie 1 and 2 indexes of the appropriate genome assembly if you will be running Rail-RNA in either its single-computer (local) or IPython Parallel (parallel) modes. The easiest way to get these is by downloading an [Illumina iGenome](http://support.illumina.com/sequencing/sequencing_software/igenome.html). If running Rail-RNA on EMR (elastic mode) and aligning to hg19, the assembly can be specified at the command line with the `-a` parameter.
 

src/rna/driver/rail-rna.txt

@@ -1 +1 @@
-∀ Rail-RNA v0.2.3a
+∀ Rail-RNA v0.2.3b

src/rna/driver/rna_config.py

@@ -2605,9 +2605,9 @@ def __init__(self, base, check_manifest=False,
 printf '\\nexport HOME=/home/hadoop\\n' >>/home/hadoop/conf/hadoop-user-env.sh
 sudo ln -s /home/hadoop/.s3cfg /home/.s3cfg
 
-curl -OL https://github.com/s3tools/s3cmd/releases/download/v1.5.2/s3cmd-1.5.2.tar.gz
-tar xvzf s3cmd-1.5.2.tar.gz
-cd s3cmd-1.5.2
+curl -OL https://github.com/s3tools/s3cmd/releases/download/v1.6.1/s3cmd-1.6.1.tar.gz
+tar xvzf s3cmd-1.6.1.tar.gz
+cd s3cmd-1.6.1
 sudo ln -s $(pwd)/s3cmd /usr/bin/s3cmd
 
 cat >~/.s3cfg <<EOF

src/rna/utils/filemover.py

@@ -69,7 +69,8 @@ def put(self, filename, url):
                 command_list.append("--acl-public")
             command_list.extend(
                     [filename, url.to_nonnative_url(),
-                        '--server-side-encryption']
+                        '--server-side-encryption',
+                        '--stop-on-error']
                 )
         elif url.is_curlable:
             raise RuntimeError('Can\'t upload to http/ftp URLs.')