changeset 12:aab6cf87b40a draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust commit 8a847f019b21abaf4de2612dead57163b2c92d81
author rnateam
date Mon, 19 Nov 2018 08:10:14 -0500
parents 6ecd674b5b62
children dbb6ee3179bc
files blockclust.xml test-data/test.bam test-data/test.tabular tool_dependencies.xml
diffstat 4 files changed, 2223 insertions(+), 188 deletions(-) [+]
line wrap: on
line diff
--- a/blockclust.xml	Tue Feb 03 08:08:49 2015 -0500
+++ b/blockclust.xml	Mon Nov 19 08:10:14 2018 -0500
@@ -1,74 +1,43 @@
-<tool id="blockclust" name="BlockClust" version="1.0.0">
+<tool id="blockclust" name="BlockClust" version="1.1.0">
     <description>efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles</description>
     <requirements>
-        <requirement type="package" version="1.0">blockclust</requirement>
-        <requirement type="package" version="1.1">eden</requirement>
-        <requirement type="package" version="3.0.3">R</requirement>
-        <requirement type="package" version="0.1.19">samtools</requirement>
-        <requirement type="package" version="12.135">mcl</requirement>
-        <requirement type="package" version="1.0">blockclust_rlibs</requirement>
+        <requirement type="package" version="1.1.0">blockclust</requirement>
     </requirements>
-    <version_command>echo '1.0'</version_command>
-    <command>
-<![CDATA[
+    <version_command>blockclust.py -v</version_command>
+    <command detect_errors="aggressive"><![CDATA[
+        export BLOCKCLUST_DATA_PATH=\$(dirname \$(which blockclust.py))/../share/blockclust_data &&
+
         #if str($tool_mode.operation) == "pre":
-            BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed
-        #elif str($tool_mode.operation) == "clust":
+            ln -s '$tool_mode.reads_bam' reads.bam &&
+            ln -f -s '${$tool_mode.reads_bam.metadata.bam_index}' reads.bam.bai &&
+            blockclust.py 
+                -m PRE -bam reads.bam
+                -tbed '$tags_bed'
+        #elif str($tool_mode.operation) == "analysis":
             #set $outputdir = $clusters.files_path
-            #set $accept_bed=list()
-            #set $reject_bed=list()
-            ## prepare annotations
-            #if str($tool_mode.reference) == "hg19":
-                $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.accept.bed")
-                $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.reject.bed")
-            #elif str($tool_mode.reference) == "mm10":
-                $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.accept.bed")
-                $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.reject.bed")
-            #elif str($tool_mode.reference) == "dm3":
-                $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.accept.bed")
-                $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.reject.bed")
-                #elif str($tool_mode.reference) == "rheMac3":
-                $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/rheMac3/rheMac3.accept.bed")
-                $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/rheMac3/rheMac3.reject.bed")
-            #elif str($tool_mode.reference) == "panTro4":
-                $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/panTro3/panTro4.accept.bed")
-                $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/panTro3/panTro4.reject.bed")
-            #elif str($tool_mode.reference) == "xenTro3":
-                $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/xenTro3/xenTro3.accept.bed")
-                $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/xenTro3/xenTro3.reject.bed")
-            #elif str($tool_mode.reference) == "celWS235":
-                $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.accept.bed")
-                $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.reject.bed")
-            #elif str($tool_mode.reference) == "tair10":
-                $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.accept.bed")
-                $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.reject.bed")
-            #end if
-            BlockClustPipeLine.pl -m TEST -c \$BLOCKCLUST_DATA_PATH/blockclust.config
+            blockclust.py 
+            -o ./
+            -m ANALYSIS
+            -f "\$BLOCKCLUST_DATA_PATH/blockclust.config"
             -t $tool_mode.input_bbo
-            -a #echo ''.join( $accept_bed )
-            -r #echo ''.join( $reject_bed )
-            -o $outputdir
+            -a "\$BLOCKCLUST_DATA_PATH/$tool_mode.reference/${tool_mode.reference}.accept.bed"
+            -r "\$BLOCKCLUST_DATA_PATH/$tool_mode.reference/${tool_mode.reference}.reject.bed"
             #if $tool_mode.nochr:
                 -nochr
             #end if
             #if str($tool_mode.pred.enable_pred) == "yes":
-                -p
-                -pm $tool_mode.pred.pred_mode
-                -md \$BLOCKCLUST_DATA_PATH/models;
-                #if str($tool_mode.pred.pred_mode) == "nearest_neighbour":
-                    cp #echo os.path.join($outputdir,'nearest_neighbour_predictions.txt')# $nearest_neighbour_pred_bed;
-                #elif str($tool_mode.pred.pred_mode) == "model_based":
-                    cp #echo os.path.join($outputdir,'model_based_predictions.txt')# $model_based_pred_bed;
-                #end if
-            #else:
-                ;
+                -c
+                -cm $tool_mode.pred.pred_mode
+                -md "\$BLOCKCLUST_DATA_PATH/models"
             #end if
-
-            cp #echo os.path.join($outputdir, 'mcl_clusters','all_clusters.bed')# $clusters;
-            cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot;
-            cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out
         #elif str($tool_mode.operation) == "post":
-            BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -rfam \$BLOCKCLUST_DATA_PATH/rfam_map.txt -o ./;
+            blockclust.py
+                -m POST 
+                -cbed '$tool_mode.clusters_bed'
+                -cs '$tool_mode.cmsearch_out'
+                -tab '$tool_mode.sim_tab_in'
+                -rfam "\$BLOCKCLUST_DATA_PATH/rfam_map.txt"
+                -o ./
         #end if
 ]]>
     </command>
@@ -76,13 +45,13 @@
         <conditional name="tool_mode">
             <param name="operation" type="select" label="Select mode of operation">
                 <option value="pre">Pre-processing </option>
-                <option value="clust">Clustering and classification</option>
+                <option value="analysis">Clustering and classification</option>
                 <option value="post">Post-processing</option>
             </param>
             <when value="pre">
                 <param name="reads_bam" type="data" format="bam" label="BAM file containing alignments" />
             </when>
-            <when value="clust">
+            <when value="analysis">
                 <param name="input_bbo" type="data" format="tabular" label="Input blockgroups file" />
                 <param name="reference" type="select" label="Select reference genome">
                     <option value="hg19">Human (hg19)</option>
@@ -102,8 +71,8 @@
                     </param>
                     <when value="yes">
                         <param name="pred_mode" type="select" label="Mode of classification">
-                            <option value="model_based">Model based</option>
-                            <option value="nearest_neighbour">Nearest neighbour</option>
+                            <option value="MODEL">Model based</option>
+                            <option value="NEAREST">Nearest neighbour</option>
                         </param>
                     </when>
                 </conditional>
@@ -118,42 +87,101 @@
 
     <outputs>
         <data format="bed" name="tags_bed" label="BlockClust: BAM to BED on ${on_string}">
-            <filter> tool_mode["operation"]=="pre"</filter>
+            <filter>tool_mode["operation"]=="pre"</filter>
         </data>
-        <data format="pdf" name="hclust_plot" label="BlockClust: Hierarchical clustering plot on ${on_string}" >
-            <filter> tool_mode["operation"]=="clust"</filter>
+        <data format="pdf" name="hclust_plot" from_work_dir="hclust_tree.pdf" label="BlockClust: Hierarchical clustering plot on ${on_string}" >
+            <filter>tool_mode["operation"]=="analysis"</filter>
         </data>
-        <data format="bed" name="clusters" label="BlockClust: BED of predicted clusters on ${on_string}">
-            <filter> tool_mode["operation"]=="clust"</filter>
+        <data format="bed" name="clusters" from_work_dir="mcl_clusters/all_clusters.bed" label="BlockClust: BED of predicted clusters on ${on_string}">
+            <filter>tool_mode["operation"]=="analysis"</filter>
         </data>
-        <data format="bed" name="model_based_pred_bed" label="BlockClust: Model based predictions BED on ${on_string}">
+        <data format="bed" name="model_based_pred_bed" from_work_dir="model_based_predictions.txt" label="BlockClust: Model based predictions BED on ${on_string}">
             <filter>
             ((
-                tool_mode["operation"] == 'clust' and
+                tool_mode["operation"] == 'analysis' and
                 tool_mode["pred"]["enable_pred"] == "yes" and
-                tool_mode["pred"]["pred_mode"] == "model_based"
+                tool_mode["pred"]["pred_mode"] == "MODEL"
+             ))
+             </filter>
+        </data>
+        <data format="bed" name="nearest_neighbour_pred_bed" from_work_dir="nearest_neighbour_predictions.txt" label="BlockClust: Nearest neighbor predictions BED on ${on_string}">
+            <filter>
+            ((
+                tool_mode["operation"] == 'analysis' and
+                tool_mode["pred"]["enable_pred"] == "yes" and
+                tool_mode["pred"]["pred_mode"] == "NEAREST"
              ))
              </filter>
         </data>
-        <data format="bed" name="nearest_neighbour_pred_bed" label="BlockClust: Nearest neighbor predictions BED on ${on_string}">
-            <filter>
-            ((
-                tool_mode["operation"] == 'clust' and
-                tool_mode["pred"]["enable_pred"] == "yes" and
-                tool_mode["pred"]["pred_mode"] == "nearest_neighbour"
-             ))
-             </filter>
-        </data>
-        <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}">
-            <filter> tool_mode["operation"]=="clust"</filter>
+        <data format="tabular" name="sim_tab_out" from_work_dir="discretized.gspan.tab" label="BlockClust: Pairwise similarities on ${on_string}">
+            <filter>tool_mode["operation"]=="analysis"</filter>
         </data>
         <data format="pdf" name="cluster_dist" from_work_dir="cluster_distribution.pdf" label="BlockClust: Cluster distribution on ${on_string}" >
-            <filter> tool_mode["operation"]=="post"</filter>
+            <filter>tool_mode["operation"]=="post"</filter>
         </data>
         <data format="pdf" name="cluster_hclust" from_work_dir="hclust_tree_clusters.pdf" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" >
-            <filter> tool_mode["operation"]=="post"</filter>
+            <filter>tool_mode["operation"]=="post"</filter>
         </data>
     </outputs>
+    <tests>
+        <!-- Test: PRE mode -->
+
+        <test expect_num_outputs="1">
+            <param name="operation" value="pre"/>
+            <param name="reads_bam" value="test.bam"/>
+            <output name="tags_bed">
+                <assert_contents>
+                    <has_text_matching expression="chr6\t26555497\t26555527\ttag_10|1|19\t0.052632\t+" />
+                    <has_text_matching expression="chr11\t122017275\t122017297\ttag_30|1|3\t0.333333\t-" />
+                </assert_contents>
+            </output>
+        </test>
+
+        <!-- Test: Clustering only -->
+        <test expect_num_outputs="3">
+            <param name="operation" value="analysis"/>
+            <param name="input_bbo" value="test.tabular"/>
+            <param name="reference" value="hg19"/>
+            <param name="enable_pred" value="no"/>
+            <output name="clusters">
+                <assert_contents>
+                    <has_text_matching expression="chr1\t173833959\t173834043\t10:snoRNA_CD-box:blockgroup_939:cluster_1\t451.50\t-" />
+                    <has_text_matching expression="chr13\t92003008\t92003075\t8:miRNA:blockgroup_256:cluster_3\t2950.50\t\+" />
+                </assert_contents>
+            </output>
+        </test>
+
+        <!-- Test: Model based prediction -->
+
+        <test expect_num_outputs="4">
+            <param name="operation" value="analysis"/>
+            <param name="input_bbo" value="test.tabular"/>
+            <param name="reference" value="hg19"/>
+            <param name="enable_pred" value="yes"/>
+            <param name="pred_mode" value="MODEL"/>
+            <output name="model_based_pred_bed">
+                <assert_contents>
+                    <has_text_matching expression="chr2\t203211000\t203211097\tpredicted_tRNA\t284.07\t-" />
+                </assert_contents>
+            </output>
+        </test>
+    
+        <!-- Test: Nearest neighbour based prediction -->
+
+        <test expect_num_outputs="4">
+            <param name="operation" value="analysis"/>
+            <param name="input_bbo" value="test.tabular"/>
+            <param name="reference" value="hg19"/>
+            <param name="enable_pred" value="yes"/>
+            <param name="pred_mode" value="NEAREST"/>
+            <output name="nearest_neighbour_pred_bed">
+                <assert_contents>
+                    <has_text_matching expression="chr2\t203211000\t203211097\tpredicted_tRNA\t284.07\t-" />
+                </assert_contents>
+            </output>
+        </test>
+
+    </tests>
     <help>
 <![CDATA[
 
Binary file test-data/test.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.tabular	Mon Nov 19 08:10:14 2018 -0500
@@ -0,0 +1,2111 @@
+>cluster_939	chr1	173833959	173834043	-	451.50	51	3
+chr1	173833973	173834009	tag_494715|1	1.000000	-	1
+chr1	173833970	173833996	tag_615439|1	1.000000	-	1
+chr1	173833970	173833996	tag_615372|1	1.000000	-	1
+chr1	173833970	173834004	tag_604763|1	1.000000	-	1
+chr1	173833970	173833992	tag_1773442|1	1.000000	-	1
+chr1	173833970	173833996	tag_1086667|1	1.000000	-	1
+chr1	173833970	173833991	tag_445309|1	1.000000	-	1
+chr1	173833970	173833999	tag_986404|1	1.000000	-	1
+chr1	173833970	173834000	tag_959571|1	1.000000	-	1
+chr1	173833970	173833993	tag_907644|1	1.000000	-	1
+chr1	173833970	173833998	tag_885788|1	1.000000	-	1
+chr1	173833970	173834000	tag_877925|1	1.000000	-	1
+chr1	173833970	173833991	tag_870314|1	1.000000	-	1
+chr1	173833970	173833996	tag_817326|1	1.000000	-	1
+chr1	173833970	173833992	tag_1436162|1	0.500000	-	1
+chr1	173833970	173834002	tag_180348|2	2.000000	-	1
+chr1	173833970	173834000	tag_54619|6	6.000000	-	1
+chr1	173833970	173833990	tag_31437|11	11.000000	-	1
+chr1	173833970	173833997	tag_21828|17	17.000000	-	1
+chr1	173833970	173833998	tag_18525|20	20.000000	-	1
+chr1	173833970	173833993	tag_17806|21	21.000000	-	1
+chr1	173833970	173833994	tag_15560|25	25.000000	-	1
+chr1	173833970	173833995	tag_15220|26	26.000000	-	1
+chr1	173833970	173834001	tag_12856|32	32.000000	-	1
+chr1	173833970	173833999	tag_11760|35	35.000000	-	1
+chr1	173833970	173833989	tag_10226|42	42.000000	-	1
+chr1	173833970	173833991	tag_9416|47	47.000000	-	1
+chr1	173833970	173833996	tag_9315|47	47.000000	-	1
+chr1	173833970	173833992	tag_7304|64	64.000000	-	1
+chr1	173833969	173833996	tag_1397646|1	1.000000	-	1
+chr1	173833968	173834002	tag_821710|1	1.000000	-	1
+chr1	173833965	173833999	tag_252059|1	1.000000	-	1
+chr1	173833964	173833996	tag_421525|1	1.000000	-	1
+chr1	173833962	173833995	tag_336214|1	1.000000	-	1
+chr1	173833960	173833992	tag_1861751|1	1.000000	-	1
+chr1	173833960	173833992	tag_482224|1	1.000000	-	1
+chr1	173833959	173833992	tag_392974|1	1.000000	-	1
+chr1	173833959	173833992	tag_709126|1	1.000000	-	1
+chr1	173834019	173834043	tag_519261|1	1.000000	-	2
+chr1	173834018	173834042	tag_1772046|1	1.000000	-	2
+chr1	173834015	173834042	tag_653136|1	1.000000	-	2
+chr1	173834014	173834042	tag_873957|1	1.000000	-	2
+chr1	173834013	173834042	tag_1701612|1	1.000000	-	2
+chr1	173834012	173834042	tag_1612183|1	1.000000	-	2
+chr1	173834008	173834043	tag_1774651|1	1.000000	-	2
+chr1	173834007	173834043	tag_1420129|1	1.000000	-	2
+chr1	173834007	173834043	tag_139153|2	2.000000	-	2
+chr1	173834006	173834042	tag_1054353|1	1.000000	-	2
+chr1	173834006	173834042	tag_18530|20	20.000000	-	2
+chr1	173834023	173834042	tag_885887|1	1.000000	-	3
+chr1	173834021	173834042	tag_549350|1	1.000000	-	3
+>cluster_940	chr1	173834480	173834567	-	354.50	46	4
+chr1	173834490	173834511	tag_1307815|1	1.000000	-	1
+chr1	173834490	173834509	tag_2551|227	227.000000	-	1
+chr1	173834488	173834507	tag_104865|3	3.000000	-	1
+chr1	173834488	173834509	tag_104283|3	3.000000	-	1
+chr1	173834488	173834508	tag_1332791|1	1.000000	-	1
+chr1	173834487	173834508	tag_876963|1	1.000000	-	1
+chr1	173834487	173834507	tag_37578|9	9.000000	-	1
+chr1	173834487	173834509	tag_23539|15	15.000000	-	1
+chr1	173834481	173834507	tag_714997|1	1.000000	-	1
+chr1	173834548	173834567	tag_313337|1	1.000000	-	2
+chr1	173834547	173834567	tag_1079769|1	0.500000	-	2
+chr1	173834547	173834566	tag_401803|1	1.000000	-	2
+chr1	173834547	173834567	tag_42263|8	8.000000	-	2
+chr1	173834546	173834567	tag_1849484|1	0.500000	-	2
+chr1	173834546	173834566	tag_381674|1	1.000000	-	2
+chr1	173834543	173834567	tag_983219|1	1.000000	-	2
+chr1	173834542	173834567	tag_94884|3	3.000000	-	2
+chr1	173834540	173834567	tag_621110|1	1.000000	-	2
+chr1	173834539	173834567	tag_421538|1	1.000000	-	2
+chr1	173834539	173834566	tag_234286|1	1.000000	-	2
+chr1	173834538	173834566	tag_560176|1	1.000000	-	2
+chr1	173834538	173834566	tag_1789529|1	1.000000	-	2
+chr1	173834538	173834567	tag_1073342|1	1.000000	-	2
+chr1	173834537	173834567	tag_1442897|1	1.000000	-	2
+chr1	173834537	173834567	tag_157484|2	2.000000	-	2
+chr1	173834537	173834566	tag_27201|13	13.000000	-	2
+chr1	173834536	173834566	tag_895368|1	1.000000	-	2
+chr1	173834535	173834566	tag_1196414|1	1.000000	-	2
+chr1	173834534	173834566	tag_107479|3	3.000000	-	2
+chr1	173834534	173834567	tag_676425|1	1.000000	-	2
+chr1	173834533	173834567	tag_222644|1	1.000000	-	2
+chr1	173834532	173834566	tag_56426|5	5.000000	-	2
+chr1	173834532	173834567	tag_25820|14	14.000000	-	2
+chr1	173834524	173834566	tag_804228|1	1.000000	-	2
+chr1	173834511	173834539	tag_883402|1	1.000000	-	3
+chr1	173834509	173834535	tag_1025251|1	1.000000	-	3
+chr1	173834509	173834540	tag_171208|2	2.000000	-	3
+chr1	173834509	173834539	tag_75815|4	4.000000	-	3
+chr1	173834509	173834537	tag_33421|10	10.000000	-	3
+chr1	173834508	173834537	tag_247501|1	1.000000	-	3
+chr1	173834507	173834539	tag_480285|1	1.000000	-	3
+chr1	173834504	173834537	tag_74276|4	4.000000	-	3
+chr1	173834499	173834535	tag_1496397|1	1.000000	-	3
+chr1	173834498	173834539	tag_1180496|1	0.500000	-	3
+chr1	173834497	173834532	tag_779265|1	1.000000	-	3
+chr1	173834480	173834502	tag_180513|2	2.000000	-	4
+>cluster_1036	chr20	2634857	2634939	+	219.00	41	3
+chr20	2634911	2634933	tag_480211|1	1.000000	+	1
+chr20	2634911	2634930	tag_137167|2	2.000000	+	1
+chr20	2634909	2634932	tag_1910963|1	1.000000	+	1
+chr20	2634909	2634931	tag_1038415|1	1.000000	+	1
+chr20	2634909	2634932	tag_651181|1	1.000000	+	1
+chr20	2634907	2634931	tag_932933|1	1.000000	+	1
+chr20	2634906	2634931	tag_145487|2	2.000000	+	1
+chr20	2634906	2634930	tag_72902|4	4.000000	+	1
+chr20	2634905	2634931	tag_292125|1	1.000000	+	1
+chr20	2634905	2634930	tag_263191|1	1.000000	+	1
+chr20	2634903	2634930	tag_1907344|1	1.000000	+	1
+chr20	2634903	2634930	tag_1887120|1	1.000000	+	1
+chr20	2634903	2634935	tag_571653|1	1.000000	+	1
+chr20	2634903	2634930	tag_1149396|1	1.000000	+	1
+chr20	2634903	2634937	tag_551396|1	1.000000	+	1
+chr20	2634903	2634930	tag_1141171|1	1.000000	+	1
+chr20	2634903	2634930	tag_1793057|1	1.000000	+	1
+chr20	2634903	2634930	tag_483937|1	1.000000	+	1
+chr20	2634903	2634930	tag_403469|1	1.000000	+	1
+chr20	2634903	2634930	tag_400865|1	1.000000	+	1
+chr20	2634903	2634931	tag_902424|1	1.000000	+	1
+chr20	2634903	2634939	tag_854785|1	1.000000	+	1
+chr20	2634903	2634937	tag_1475911|1	1.000000	+	1
+chr20	2634903	2634932	tag_213180|1	1.000000	+	1
+chr20	2634903	2634937	tag_1416825|1	1.000000	+	1
+chr20	2634903	2634931	tag_1412864|1	1.000000	+	1
+chr20	2634903	2634929	tag_762145|1	1.000000	+	1
+chr20	2634903	2634930	tag_1318744|1	1.000000	+	1
+chr20	2634903	2634931	tag_22179|16	16.000000	+	1
+chr20	2634903	2634930	tag_4169|128	128.000000	+	1
+chr20	2634902	2634939	tag_603145|1	1.000000	+	1
+chr20	2634902	2634930	tag_354254|1	1.000000	+	1
+chr20	2634902	2634931	tag_93609|3	3.000000	+	1
+chr20	2634902	2634930	tag_13997|28	28.000000	+	1
+chr20	2634901	2634931	tag_110382|3	3.000000	+	1
+chr20	2634898	2634932	tag_1870610|1	1.000000	+	1
+chr20	2634898	2634931	tag_417772|1	1.000000	+	1
+chr20	2634898	2634930	tag_1004990|1	1.000000	+	1
+chr20	2634857	2634881	tag_1918220|1	1.000000	+	2
+chr20	2634857	2634893	tag_1459784|1	1.000000	+	2
+chr20	2634891	2634915	tag_652486|1	1.000000	+	3
+>cluster_256	chr13	92003008	92003075	+	2950.50	110	2
+chr13	92003014	92003033	tag_1641733|1	1.000000	+	1
+chr13	92003013	92003032	tag_149732|2	2.000000	+	1
+chr13	92003013	92003033	tag_1389853|1	1.000000	+	1
+chr13	92003012	92003033	tag_155031|2	2.000000	+	1
+chr13	92003012	92003032	tag_64923|5	5.000000	+	1
+chr13	92003011	92003032	tag_136417|2	2.000000	+	1
+chr13	92003010	92003033	tag_1547427|1	1.000000	+	1
+chr13	92003010	92003032	tag_198355|2	2.000000	+	1
+chr13	92003009	92003032	tag_1273727|1	1.000000	+	1
+chr13	92003009	92003032	tag_1914082|1	1.000000	+	1
+chr13	92003009	92003032	tag_1236428|1	1.000000	+	1
+chr13	92003009	92003041	tag_1873034|1	1.000000	+	1
+chr13	92003009	92003032	tag_1866503|1	1.000000	+	1
+chr13	92003009	92003042	tag_601156|1	1.000000	+	1
+chr13	92003009	92003032	tag_1195382|1	1.000000	+	1
+chr13	92003009	92003032	tag_1180165|1	1.000000	+	1
+chr13	92003009	92003033	tag_579011|1	1.000000	+	1
+chr13	92003009	92003033	tag_574678|1	1.000000	+	1
+chr13	92003009	92003033	tag_1822900|1	0.500000	+	1
+chr13	92003009	92003032	tag_1157640|1	1.000000	+	1
+chr13	92003009	92003032	tag_1813212|1	1.000000	+	1
+chr13	92003009	92003032	tag_1812673|1	1.000000	+	1
+chr13	92003009	92003034	tag_1154627|1	1.000000	+	1
+chr13	92003009	92003032	tag_544427|1	1.000000	+	1
+chr13	92003009	92003032	tag_1784778|1	1.000000	+	1
+chr13	92003009	92003032	tag_1115765|1	1.000000	+	1
+chr13	92003009	92003033	tag_1112838|1	1.000000	+	1
+chr13	92003009	92003034	tag_1078321|1	1.000000	+	1
+chr13	92003009	92003032	tag_1047694|1	0.500000	+	1
+chr13	92003009	92003032	tag_1701810|1	1.000000	+	1
+chr13	92003009	92003032	tag_1697631|1	1.000000	+	1
+chr13	92003009	92003032	tag_1039938|1	1.000000	+	1
+chr13	92003009	92003033	tag_440901|1	1.000000	+	1
+chr13	92003009	92003033	tag_419655|1	1.000000	+	1
+chr13	92003009	92003032	tag_408370|1	1.000000	+	1
+chr13	92003009	92003033	tag_394497|1	1.000000	+	1
+chr13	92003009	92003040	tag_980403|1	1.000000	+	1
+chr13	92003009	92003033	tag_1636555|1	1.000000	+	1
+chr13	92003009	92003032	tag_378710|1	1.000000	+	1
+chr13	92003009	92003033	tag_932492|1	1.000000	+	1
+chr13	92003009	92003032	tag_1583543|1	1.000000	+	1
+chr13	92003009	92003032	tag_333404|1	1.000000	+	1
+chr13	92003009	92003032	tag_320097|1	1.000000	+	1
+chr13	92003009	92003032	tag_318336|1	1.000000	+	1
+chr13	92003009	92003032	tag_311510|1	1.000000	+	1
+chr13	92003009	92003032	tag_1557059|1	0.500000	+	1
+chr13	92003009	92003032	tag_865326|1	1.000000	+	1
+chr13	92003009	92003032	tag_1518741|1	1.000000	+	1
+chr13	92003009	92003032	tag_269186|1	1.000000	+	1
+chr13	92003009	92003032	tag_860222|1	1.000000	+	1
+chr13	92003009	92003035	tag_240673|1	1.000000	+	1
+chr13	92003009	92003045	tag_230885|1	1.000000	+	1
+chr13	92003009	92003040	tag_1473996|1	1.000000	+	1
+chr13	92003009	92003028	tag_196465|2	1.000000	+	1
+chr13	92003009	92003032	tag_193308|2	2.000000	+	1
+chr13	92003009	92003032	tag_191484|2	2.000000	+	1
+chr13	92003009	92003032	tag_185834|2	2.000000	+	1
+chr13	92003009	92003032	tag_184913|2	2.000000	+	1
+chr13	92003009	92003032	tag_178736|2	2.000000	+	1
+chr13	92003009	92003032	tag_176955|2	2.000000	+	1
+chr13	92003009	92003032	tag_175554|2	2.000000	+	1
+chr13	92003009	92003032	tag_1425258|1	1.000000	+	1
+chr13	92003009	92003034	tag_171164|2	2.000000	+	1
+chr13	92003009	92003032	tag_168623|2	2.000000	+	1
+chr13	92003009	92003033	tag_1416893|1	1.000000	+	1
+chr13	92003009	92003033	tag_768859|1	1.000000	+	1
+chr13	92003009	92003032	tag_158620|2	2.000000	+	1
+chr13	92003009	92003033	tag_156672|2	2.000000	+	1
+chr13	92003009	92003032	tag_150638|2	2.000000	+	1
+chr13	92003009	92003032	tag_140266|2	2.000000	+	1
+chr13	92003009	92003033	tag_131963|2	2.000000	+	1
+chr13	92003009	92003040	tag_722677|1	1.000000	+	1
+chr13	92003009	92003032	tag_95639|3	3.000000	+	1
+chr13	92003009	92003032	tag_1356131|1	1.000000	+	1
+chr13	92003009	92003032	tag_90478|3	3.000000	+	1
+chr13	92003009	92003033	tag_86763|3	3.000000	+	1
+chr13	92003009	92003032	tag_85156|3	3.000000	+	1
+chr13	92003009	92003035	tag_706425|1	1.000000	+	1
+chr13	92003009	92003032	tag_83071|4	4.000000	+	1
+chr13	92003009	92003032	tag_76538|4	4.000000	+	1
+chr13	92003009	92003036	tag_73033|4	4.000000	+	1
+chr13	92003009	92003040	tag_64478|5	5.000000	+	1
+chr13	92003009	92003033	tag_690310|1	1.000000	+	1
+chr13	92003009	92003033	tag_57937|5	5.000000	+	1
+chr13	92003009	92003032	tag_45115|7	7.000000	+	1
+chr13	92003009	92003032	tag_37103|9	9.000000	+	1
+chr13	92003009	92003031	tag_33411|10	10.000000	+	1
+chr13	92003009	92003030	tag_32826|10	10.000000	+	1
+chr13	92003009	92003032	tag_31268|11	11.000000	+	1
+chr13	92003009	92003029	tag_29853|11	11.000000	+	1
+chr13	92003009	92003033	tag_659619|1	1.000000	+	1
+chr13	92003009	92003033	tag_2279|260	260.000000	+	1
+chr13	92003009	92003032	tag_349|2385	2385.000000	+	1
+chr13	92003008	92003033	tag_1217305|1	1.000000	+	1
+chr13	92003008	92003032	tag_1106560|1	1.000000	+	1
+chr13	92003051	92003073	tag_431229|1	1.000000	+	2
+chr13	92003050	92003071	tag_625979|1	1.000000	+	2
+chr13	92003050	92003073	tag_1671946|1	1.000000	+	2
+chr13	92003050	92003074	tag_1660313|1	1.000000	+	2
+chr13	92003050	92003073	tag_1501997|1	1.000000	+	2
+chr13	92003050	92003075	tag_1484024|1	1.000000	+	2
+chr13	92003050	92003073	tag_734771|1	1.000000	+	2
+chr13	92003050	92003073	tag_1369683|1	1.000000	+	2
+chr13	92003050	92003074	tag_107587|3	3.000000	+	2
+chr13	92003050	92003073	tag_708879|1	1.000000	+	2
+chr13	92003050	92003074	tag_80587|4	4.000000	+	2
+chr13	92003050	92003073	tag_39212|8	8.000000	+	2
+chr13	92003050	92003072	tag_26711|13	13.000000	+	2
+chr13	92003050	92003073	tag_23644|15	15.000000	+	2
+chr13	92003050	92003073	tag_7390|63	63.000000	+	2
+>cluster_1082	chr21	17911414	17911480	+	2244.00	98	2
+chr21	17911421	17911443	tag_614425|1	1.000000	+	1
+chr21	17911421	17911442	tag_1793809|1	1.000000	+	1
+chr21	17911421	17911441	tag_350949|1	1.000000	+	1
+chr21	17911421	17911441	tag_252923|1	1.000000	+	1
+chr21	17911420	17911441	tag_1260282|1	1.000000	+	1
+chr21	17911420	17911443	tag_1256565|1	1.000000	+	1
+chr21	17911420	17911443	tag_1900753|1	1.000000	+	1
+chr21	17911420	17911442	tag_1883668|1	1.000000	+	1
+chr21	17911420	17911444	tag_1221262|1	1.000000	+	1
+chr21	17911420	17911441	tag_618174|1	1.000000	+	1
+chr21	17911420	17911441	tag_1859833|1	1.000000	+	1
+chr21	17911420	17911441	tag_1855395|1	1.000000	+	1
+chr21	17911420	17911441	tag_596516|1	1.000000	+	1
+chr21	17911420	17911443	tag_1850718|1	1.000000	+	1
+chr21	17911420	17911441	tag_1827304|1	1.000000	+	1
+chr21	17911420	17911443	tag_1821876|1	1.000000	+	1
+chr21	17911420	17911441	tag_1819170|1	1.000000	+	1
+chr21	17911420	17911444	tag_551437|1	1.000000	+	1
+chr21	17911420	17911442	tag_534231|1	1.000000	+	1
+chr21	17911420	17911441	tag_1766803|1	1.000000	+	1
+chr21	17911420	17911441	tag_1077841|1	1.000000	+	1
+chr21	17911420	17911441	tag_1731260|1	1.000000	+	1
+chr21	17911420	17911444	tag_1730441|1	1.000000	+	1
+chr21	17911420	17911442	tag_1728781|1	1.000000	+	1
+chr21	17911420	17911445	tag_1727368|1	1.000000	+	1
+chr21	17911420	17911443	tag_461622|1	1.000000	+	1
+chr21	17911420	17911441	tag_1051149|1	1.000000	+	1
+chr21	17911420	17911444	tag_438252|1	1.000000	+	1
+chr21	17911420	17911441	tag_1686506|1	0.500000	+	1
+chr21	17911420	17911441	tag_429645|1	1.000000	+	1
+chr21	17911420	17911442	tag_1677951|1	1.000000	+	1
+chr21	17911420	17911443	tag_1015680|1	0.500000	+	1
+chr21	17911420	17911442	tag_1006423|1	1.000000	+	1
+chr21	17911420	17911447	tag_995490|1	1.000000	+	1
+chr21	17911420	17911442	tag_396868|1	1.000000	+	1
+chr21	17911420	17911441	tag_964617|1	1.000000	+	1
+chr21	17911420	17911442	tag_961711|1	1.000000	+	1
+chr21	17911420	17911442	tag_356318|1	1.000000	+	1
+chr21	17911420	17911443	tag_1605240|1	1.000000	+	1
+chr21	17911420	17911446	tag_1604265|1	1.000000	+	1
+chr21	17911420	17911441	tag_343498|1	1.000000	+	1
+chr21	17911420	17911441	tag_931201|1	1.000000	+	1
+chr21	17911420	17911441	tag_332639|1	1.000000	+	1
+chr21	17911420	17911442	tag_309627|1	1.000000	+	1
+chr21	17911420	17911441	tag_1533391|1	1.000000	+	1
+chr21	17911420	17911443	tag_866682|1	0.500000	+	1
+chr21	17911420	17911443	tag_865948|1	0.500000	+	1
+chr21	17911420	17911441	tag_257335|1	1.000000	+	1
+chr21	17911420	17911441	tag_1504991|1	1.000000	+	1
+chr21	17911420	17911443	tag_804590|1	1.000000	+	1
+chr21	17911420	17911441	tag_799259|1	1.000000	+	1
+chr21	17911420	17911443	tag_196978|2	2.000000	+	1
+chr21	17911420	17911441	tag_796179|1	1.000000	+	1
+chr21	17911420	17911443	tag_195122|2	2.000000	+	1
+chr21	17911420	17911441	tag_1442626|1	1.000000	+	1
+chr21	17911420	17911443	tag_786772|1	1.000000	+	1
+chr21	17911420	17911439	tag_182477|2	2.000000	+	1
+chr21	17911420	17911447	tag_177599|2	2.000000	+	1
+chr21	17911420	17911441	tag_168684|2	2.000000	+	1
+chr21	17911420	17911441	tag_168610|2	2.000000	+	1
+chr21	17911420	17911444	tag_161446|2	2.000000	+	1
+chr21	17911420	17911441	tag_136992|2	2.000000	+	1
+chr21	17911420	17911441	tag_136422|2	2.000000	+	1
+chr21	17911420	17911443	tag_126331|2	2.000000	+	1
+chr21	17911420	17911442	tag_123836|2	2.000000	+	1
+chr21	17911420	17911441	tag_116478|2	2.000000	+	1
+chr21	17911420	17911441	tag_83240|3	3.000000	+	1
+chr21	17911420	17911443	tag_78547|4	4.000000	+	1
+chr21	17911420	17911442	tag_67234|4	4.000000	+	1
+chr21	17911420	17911441	tag_66054|5	5.000000	+	1
+chr21	17911420	17911442	tag_1332186|1	1.000000	+	1
+chr21	17911420	17911441	tag_64098|5	5.000000	+	1
+chr21	17911420	17911443	tag_687325|1	1.000000	+	1
+chr21	17911420	17911441	tag_35366|9	9.000000	+	1
+chr21	17911420	17911444	tag_27182|13	13.000000	+	1
+chr21	17911420	17911442	tag_660433|1	1.000000	+	1
+chr21	17911420	17911441	tag_1293196|1	0.500000	+	1
+chr21	17911420	17911440	tag_15840|24	24.000000	+	1
+chr21	17911420	17911442	tag_3485|158	158.000000	+	1
+chr21	17911420	17911443	tag_1654|380	380.000000	+	1
+chr21	17911420	17911441	tag_558|1405	1405.000000	+	1
+chr21	17911419	17911441	tag_1865034|1	1.000000	+	1
+chr21	17911419	17911441	tag_1158026|1	1.000000	+	1
+chr21	17911419	17911441	tag_1682168|1	1.000000	+	1
+chr21	17911419	17911441	tag_1664493|1	1.000000	+	1
+chr21	17911419	17911441	tag_178026|2	2.000000	+	1
+chr21	17911419	17911440	tag_165950|2	2.000000	+	1
+chr21	17911419	17911441	tag_7030|67	67.000000	+	1
+chr21	17911414	17911441	tag_325593|1	1.000000	+	1
+chr21	17911414	17911443	tag_288376|1	1.000000	+	1
+chr21	17911458	17911480	tag_92659|3	3.000000	+	2
+chr21	17911457	17911479	tag_1755027|1	1.000000	+	2
+chr21	17911457	17911479	tag_1742259|1	0.500000	+	2
+chr21	17911457	17911479	tag_159334|2	2.000000	+	2
+chr21	17911457	17911478	tag_745360|1	1.000000	+	2
+chr21	17911457	17911480	tag_115892|2	2.000000	+	2
+chr21	17911457	17911480	tag_58693|5	5.000000	+	2
+chr21	17911457	17911479	tag_7392|63	63.000000	+	2
+>cluster_897	chr1	156390148	156390208	-	6278.58	298	2
+chr1	156390187	156390206	tag_31805|11	3.666667	-	1
+chr1	156390186	156390206	tag_1714659|1	0.333333	-	1
+chr1	156390186	156390205	tag_181353|2	0.666667	-	1
+chr1	156390186	156390206	tag_110046|3	1.500000	-	1
+chr1	156390186	156390206	tag_5258|95	31.666667	-	1
+chr1	156390185	156390207	tag_1213436|1	0.333333	-	1
+chr1	156390185	156390206	tag_1213031|1	0.250000	-	1
+chr1	156390185	156390206	tag_1033890|1	0.333333	-	1
+chr1	156390185	156390206	tag_988101|1	0.200000	-	1
+chr1	156390185	156390206	tag_186860|2	0.666667	-	1
+chr1	156390185	156390206	tag_164996|2	0.666667	-	1
+chr1	156390185	156390206	tag_736686|1	0.333333	-	1
+chr1	156390185	156390206	tag_1369554|1	0.250000	-	1
+chr1	156390185	156390205	tag_72933|4	1.333333	-	1
+chr1	156390185	156390206	tag_36154|9	4.500000	-	1
+chr1	156390185	156390206	tag_2031|297	99.000000	-	1
+chr1	156390184	156390206	tag_1906366|1	0.333333	-	1
+chr1	156390184	156390206	tag_1193145|1	0.250000	-	1
+chr1	156390184	156390205	tag_590557|1	0.250000	-	1
+chr1	156390184	156390205	tag_1819872|1	0.333333	-	1
+chr1	156390184	156390206	tag_565050|1	0.333333	-	1
+chr1	156390184	156390206	tag_1816342|1	0.333333	-	1
+chr1	156390184	156390206	tag_1139073|1	0.333333	-	1
+chr1	156390184	156390203	tag_1127250|1	0.333333	-	1
+chr1	156390184	156390205	tag_1067000|1	0.333333	-	1
+chr1	156390184	156390206	tag_1048647|1	0.333333	-	1
+chr1	156390184	156390206	tag_938026|1	0.333333	-	1
+chr1	156390184	156390206	tag_1507760|1	0.333333	-	1
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+chr21	17911420	17911440	tag_15840|24	24.000000	+	1
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+chr21	17911420	17911443	tag_1654|380	380.000000	+	1
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+chr21	17911419	17911441	tag_7030|67	67.000000	+	1
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+chr21	17911414	17911443	tag_288376|1	1.000000	+	1
+chr21	17911458	17911480	tag_92659|3	3.000000	+	2
+chr21	17911457	17911479	tag_1755027|1	1.000000	+	2
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+chr21	17911457	17911479	tag_159334|2	2.000000	+	2
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+chr21	17911457	17911480	tag_58693|5	5.000000	+	2
+chr21	17911457	17911479	tag_7392|63	63.000000	+	2
+>cluster_1321	chr2	203211000	203211097	-	284.07	89	6
+chr2	203211078	203211097	tag_452391|1	0.500000	-	1
+chr2	203211077	203211096	tag_1031720|1	0.500000	-	1
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+chr2	203211077	203211096	tag_24908|14	7.000000	-	1
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+chr2	203211075	203211096	tag_163233|2	1.000000	-	1
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+chr2	203211074	203211096	tag_30937|11	5.500000	-	1
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+chr2	203211074	203211094	tag_9578|46	23.000000	-	1
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+chr2	203211073	203211096	tag_512465|1	0.500000	-	1
+chr2	203211073	203211094	tag_455624|1	0.333333	-	1
+chr2	203211073	203211094	tag_746765|1	0.500000	-	1
+chr2	203211072	203211096	tag_351358|1	0.500000	-	1
+chr2	203211071	203211097	tag_1663651|1	0.500000	-	1
+chr2	203211071	203211090	tag_927449|1	0.250000	-	1
+chr2	203211071	203211092	tag_893688|1	0.500000	-	1
+chr2	203211071	203211095	tag_175941|2	1.000000	-	1
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+chr2	203211070	203211091	tag_729469|1	0.500000	-	1
+chr2	203211069	203211090	tag_375480|1	0.250000	-	1
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+chr2	203211047	203211075	tag_1776657|1	0.500000	-	3
+chr2	203211046	203211079	tag_1728473|1	0.500000	-	3
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+chr2	203211000	203211023	tag_84219|3	1.500000	-	4
+chr2	203211000	203211024	tag_79090|4	2.000000	-	4
+chr2	203211000	203211019	tag_48051|6	3.000000	-	4
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+chr2	203211013	203211034	tag_331039|1	1.000000	-	6
--- a/tool_dependencies.xml	Tue Feb 03 08:08:49 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,104 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="samtools" version="0.1.19">
-        <repository changeset_revision="923adc89c666" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="R" version="3.0.3">
-        <repository changeset_revision="f386d7431fe0" name="package_r_3_0_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="eden" version="1.1">
-        <repository changeset_revision="8087eef83c35" name="package_eden_1_1" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="mcl" version="12.135">
-        <repository changeset_revision="9f59d1a59999" name="package_mcl_12_135" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="blockclust_rlibs" version="1.0">
-         <install version="1.0">
-            <actions>
-                <action type="setup_r_environment">
-                    <repository changeset_revision="f386d7431fe0" name="package_r_3_0_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-                        <package name="R" version="3.0.3" />
-                    </repository>
-                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/ape_3.0-11.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/plyr_1.8.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/digest_0.6.4.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/gtable_0.1.2.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/dichromat_2.0-0.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/colorspace_1.2-4.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/munsell_0.4.2.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/labeling_0.2.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/RColorBrewer_1.0-5.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/stringr_0.6.2.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/scales_0.2.3.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/proto_0.3-10.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/reshape2_1.2.2.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/ggplot2_0.9.3.1.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/squash_1.0.1.tar.gz</package>
-                </action>
-            </actions>
-        </install>
-        <readme>
-
-        </readme>
-    </package>
-    <package name="blockclust" version="1.0">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-1.0.tar.gz</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>BlockClust</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>BlockClustPipeLine.pl</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>filterKnownBlockGroups.pl</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>perf</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>plotClusters.R</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>blockclust.config</source>
-                    <destination>$INSTALL_DIR/data/</destination>
-                </action>
-                <action type="move_file">
-                    <source>rfam_map.txt</source>
-                    <destination>$INSTALL_DIR/data/</destination>
-                </action>
-                <action type="make_directory">$INSTALL_DIR/data/annotations</action>
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/dm3.tar.gz</action>
-                <action type="shell_command">tar xfvz dm3.tar.gz -C $INSTALL_DIR/data/annotations/</action>
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/hg19.tar.gz</action>
-                <action type="shell_command">tar xfvz hg19.tar.gz -C $INSTALL_DIR/data/annotations/</action>
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/mm10.tar.gz</action>
-                <action type="shell_command">tar xfvz mm10.tar.gz -C $INSTALL_DIR/data/annotations/</action>
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/panTro4.tar.gz</action>
-                <action type="shell_command">tar xfvz panTro4.tar.gz -C $INSTALL_DIR/data/annotations/</action>
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/rheMac3.tar.gz</action>
-                <action type="shell_command">tar xfvz rheMac3.tar.gz -C $INSTALL_DIR/data/annotations/</action>
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/celWS235.tar.gz</action>
-                <action type="shell_command">tar xfvz celWS235.tar.gz -C $INSTALL_DIR/data/annotations/</action>
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/tair10.tar.gz</action>
-                <action type="shell_command">tar xfvz tair10.tar.gz -C $INSTALL_DIR/data/annotations/</action>
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/models.tar.gz</action>
-                <action type="shell_command">tar xfvz models.tar.gz -C $INSTALL_DIR/data/</action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="set_to" name="BLOCKCLUST_DATA_PATH">$INSTALL_DIR/data</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-
-        </readme>
-    </package>
-</tool_dependency>