readme update and optim for multi_muscle_align increased

dereneaton · Mar 31, 2016 · 011aa63 · 011aa63
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diff --git a/README.rst b/README.rst
@@ -12,9 +12,9 @@ Tutorials
 
 Documentation is in the works_, for now there are working example tutorials_.
 
-.. _tutorials: http://nbviewer.ipython.org/github/dereneaton/ipyrad/tree/master/tests/
+.. _tutorials: http://ipyrad.readthedocs.org/en/latest/userguide.html
 
-.. _works: http://ipyrad.readthedocs.org/en/latest/  
+.. _works: http://ipyrad.readthedocs.org/en/latest/
 
 Installation
 ------------

diff --git a/docs/tutorial_intro_cli.rst b/docs/tutorial_intro_cli.rst
@@ -214,7 +214,7 @@ separate line with a tab between them.
 
 .. code-block:: bash
 
-    cat ./data/sim_rad_test_barcodes.txt
+    cat ./ipsimdata/sim_rad_test_barcodes.txt
 
 .. parsed-literal::
     1A_0    CATCAT

diff --git a/ipyrad/assemble/cluster_within.py b/ipyrad/assemble/cluster_within.py
@@ -779,9 +779,9 @@ def multi_muscle_align(data, sample, ipyclient):
         ## get the number of clusters
         clustfile = os.path.join(data.dirs.clusts, sample.name+".clust.gz")
         clustio = gzip.open(clustfile, 'rb')
-        optim = 100
-        if sample.stats.clusters_total > 500:
-            optim = int(sample.stats.clusters_total/len(ipyclient))//2
+        optim = 1000
+        #if sample.stats.clusters_total > 500:
+        #    optim = int(sample.stats.clusters_total/len(ipyclient))//2
         LOGGER.debug("optim for align chunks: %s", optim)
 
         ## write optim clusters to each tmp file