diff --git a/docs/content/tools/annotate.rst b/docs/content/tools/annotate.rst
index eb0a4aa4ff123d0f0ab0741d7c67f5e84d225478..3345a7dc20d382216ead496f453237cc2c9c0a7c 100755
--- a/docs/content/tools/annotate.rst
+++ b/docs/content/tools/annotate.rst
@@ -1,3 +1,5 @@
+.. _annotate:
+
 ###############
 *annotate*
 ###############
diff --git a/docs/content/tools/bamtobed.rst b/docs/content/tools/bamtobed.rst
index 2096cf526b0656b6a09983cb001e0107b71e5ec1..2cb22f86691b3efa09cd7515d1f0b91d88b72bdf 100755
--- a/docs/content/tools/bamtobed.rst
+++ b/docs/content/tools/bamtobed.rst
@@ -1,3 +1,5 @@
+.. _bamtobed:
+
 ###############
 *bamtobed*
 ###############
diff --git a/docs/content/tools/bamtofastq.rst b/docs/content/tools/bamtofastq.rst
index 3757991ddfa0ed07ee9d36a56890303cdba5f8c0..217d678fcd4db07d4e9bef91e08a2ecb22b56458 100644
--- a/docs/content/tools/bamtofastq.rst
+++ b/docs/content/tools/bamtofastq.rst
@@ -1,3 +1,5 @@
+.. _bamtofastq:
+
 ###############
 *bamtofastq*
 ###############
diff --git a/docs/content/tools/bed12tobed6.rst b/docs/content/tools/bed12tobed6.rst
index 9b41e5c9a6cb9ab9bf40e99f10650a6da65379ec..e29105b5abbdce7f444aebf4fc11a8977f435c62 100755
--- a/docs/content/tools/bed12tobed6.rst
+++ b/docs/content/tools/bed12tobed6.rst
@@ -1,3 +1,5 @@
+.. _bed12tobed6:
+
 ###############
 *bed12tobed6*
 ###############
diff --git a/docs/content/tools/bedpetobam.rst b/docs/content/tools/bedpetobam.rst
index d40e1a7d56e49458854d0674256bf682daa20dcd..92151b63042e204813cbf9f3ed768bafcc7ba42f 100644
--- a/docs/content/tools/bedpetobam.rst
+++ b/docs/content/tools/bedpetobam.rst
@@ -1,3 +1,5 @@
+.. _bedpetobam:
+
 ###############
 *bedpetobam*
-###############
\ No newline at end of file
+###############
diff --git a/docs/content/tools/bedtobam.rst b/docs/content/tools/bedtobam.rst
index 6e1183af86e01f65196e84abe46ec5f1ad039b39..3177dd0cd2b018501cadbae88fa66b569fdeb60f 100755
--- a/docs/content/tools/bedtobam.rst
+++ b/docs/content/tools/bedtobam.rst
@@ -1,3 +1,5 @@
+.. _bedtobam:
+
 ###############
 *bedtobam*
 ###############
diff --git a/docs/content/tools/closest.rst b/docs/content/tools/closest.rst
index f04495674e5b8968fda0fb2e8c94d2c34d8ab11a..aa13756646100ab4859da6d0c3fd473e7b29b4ec 100755
--- a/docs/content/tools/closest.rst
+++ b/docs/content/tools/closest.rst
@@ -1,3 +1,5 @@
+.. _closest:
+
 ###############
 *closest*
 ###############
diff --git a/docs/content/tools/cluster.rst b/docs/content/tools/cluster.rst
index 9f4f6f370f5d4951976d247a6f4f0fe618bf54be..90a5c8b9722aa348e56ac69e9b78c05960eb6917 100644
--- a/docs/content/tools/cluster.rst
+++ b/docs/content/tools/cluster.rst
@@ -1,3 +1,5 @@
+.. _cluster:
+
 ###############
 *cluster*
 ###############
diff --git a/docs/content/tools/complement.rst b/docs/content/tools/complement.rst
index 05d4abafb6469aab0a99880de57bc7bb21d328ae..a3c850f967ed0fce621cb8018b97fb664b9ccbc5 100755
--- a/docs/content/tools/complement.rst
+++ b/docs/content/tools/complement.rst
@@ -1,3 +1,5 @@
+.. _complement:
+
 ###############
 *complement*
 ###############
diff --git a/docs/content/tools/coverage.rst b/docs/content/tools/coverage.rst
index 9d884a43a01f3d32078da8cdf82cda6891b1e29a..f5de907c23952b1f62fec63f2e4a5671bf2d1f76 100755
--- a/docs/content/tools/coverage.rst
+++ b/docs/content/tools/coverage.rst
@@ -1,3 +1,5 @@
+.. _coverage:
+
 ###############
 *coverage*
 ###############
diff --git a/docs/content/tools/expand.rst b/docs/content/tools/expand.rst
index 5b0126f4371f9c9af5832a19a0e90709f4bbed53..15b53f65a6373bf42718b31f00b87c545830b163 100644
--- a/docs/content/tools/expand.rst
+++ b/docs/content/tools/expand.rst
@@ -1,3 +1,5 @@
+.. _expand:
+
 ###############
 *expand*
-###############
\ No newline at end of file
+###############
diff --git a/docs/content/tools/flank.rst b/docs/content/tools/flank.rst
index a210ef69b6beca113b42e1b702cdde0621c430ff..db3b9da46ba0cf0c137cddd24d98820e5505576d 100644
--- a/docs/content/tools/flank.rst
+++ b/docs/content/tools/flank.rst
@@ -1,3 +1,5 @@
+.. _flank:
+
 ###############
 *flank*
 ###############
diff --git a/docs/content/tools/genomecov.rst b/docs/content/tools/genomecov.rst
index e0c73a6e7449c271ea1952258a1203cc78d074f0..e5fd0553f3002f3b36cfd5f9200fb7a227e2c093 100755
--- a/docs/content/tools/genomecov.rst
+++ b/docs/content/tools/genomecov.rst
@@ -1,3 +1,5 @@
+.. _genomecov:
+
 ###############
 *genomecov*
 ###############
diff --git a/docs/content/tools/getfasta.rst b/docs/content/tools/getfasta.rst
index d9ff1046fb1c25bb3845a836ea06d087d3e5b993..7c65ceb0151fbcf94a14f4e1d5624259b2638a39 100755
--- a/docs/content/tools/getfasta.rst
+++ b/docs/content/tools/getfasta.rst
@@ -1,3 +1,5 @@
+.. _getfasta:
+
 ###############
 *getfasta*
 ###############
diff --git a/docs/content/tools/groupby.rst b/docs/content/tools/groupby.rst
index 21aa972aa6d9332fb23a9c3cdb3653cd7956990c..f28cc92f71cbac113244d54927b68dd718479cd3 100755
--- a/docs/content/tools/groupby.rst
+++ b/docs/content/tools/groupby.rst
@@ -1,3 +1,5 @@
+.. _groupby:
+
 ###############
 *groupby*
 ###############
diff --git a/docs/content/tools/igv.rst b/docs/content/tools/igv.rst
index 2b44189487db7e8fbdf7c79509504d893f329a45..2f1eb00d81fa8b02a39420046f077c2e950bcc25 100644
--- a/docs/content/tools/igv.rst
+++ b/docs/content/tools/igv.rst
@@ -1,3 +1,5 @@
+.. _igv:
+
 ###############
 *igv*
-###############
\ No newline at end of file
+###############
diff --git a/docs/content/tools/intersect.rst b/docs/content/tools/intersect.rst
index 5fda8b277dc09e27617ba671a8f7a568faae9366..735f391cba5a4dabcda0c1dc446eba2645b354c9 100755
--- a/docs/content/tools/intersect.rst
+++ b/docs/content/tools/intersect.rst
@@ -1,3 +1,5 @@
+.. _intersect:
+
 #########################################
 *intersect* 
 #########################################
diff --git a/docs/content/tools/jaccard.rst b/docs/content/tools/jaccard.rst
index 3bbf486f20b9d2d8a3e9072a8a07dca9a67e0483..268f945dab5da9335fe7bc091af6e4c72fc110c9 100644
--- a/docs/content/tools/jaccard.rst
+++ b/docs/content/tools/jaccard.rst
@@ -1,3 +1,5 @@
+.. _jaccard:
+
 ###############
 *jaccard*
 ###############
diff --git a/docs/content/tools/links.rst b/docs/content/tools/links.rst
index c1be9f14af7bf0731919bccda4d2c3d707cdb9a4..cbdbee603e759acaa44d794a219f3839266ad72f 100755
--- a/docs/content/tools/links.rst
+++ b/docs/content/tools/links.rst
@@ -1,3 +1,5 @@
+.. _links:
+
 ###############
 *links*
 ###############
diff --git a/docs/content/tools/makewindows.rst b/docs/content/tools/makewindows.rst
index a52fa27be90c89e2114b7defbb3062579d11fa3b..b95f150ff88d4e8be4163585c4295a5f0d8e2dc0 100644
--- a/docs/content/tools/makewindows.rst
+++ b/docs/content/tools/makewindows.rst
@@ -1,3 +1,5 @@
+.. _makewindows:
+
 ###############
 *makewindows*
-###############
\ No newline at end of file
+###############
diff --git a/docs/content/tools/map.rst b/docs/content/tools/map.rst
index b996f952aecec77494ac6de809a3c3f1073f761e..6ed58f5d16a09e3899cc303ca9d165ad295ab258 100644
--- a/docs/content/tools/map.rst
+++ b/docs/content/tools/map.rst
@@ -1,3 +1,5 @@
+.. _map:
+
 ###############
 *map*
 ###############
diff --git a/docs/content/tools/maskfasta.rst b/docs/content/tools/maskfasta.rst
index 157844b7849b72b8a3e0ddba75c34726fee05618..c453aca8e3c2a979ee1ad0e700f9cf281ba12cfd 100755
--- a/docs/content/tools/maskfasta.rst
+++ b/docs/content/tools/maskfasta.rst
@@ -1,3 +1,5 @@
+.. _maskfasta:
+
 ###############
 *maskfasta*
 ###############
diff --git a/docs/content/tools/merge.rst b/docs/content/tools/merge.rst
index f41b61a2ca68ac4f2afe4b197f4b0c6b26ab0d65..e6b35e84ac294cc88ebb2899db5dbc5faff26c90 100755
--- a/docs/content/tools/merge.rst
+++ b/docs/content/tools/merge.rst
@@ -1,3 +1,5 @@
+.. _merge:
+
 ###############
 *merge*
 ###############
diff --git a/docs/content/tools/multicov.rst b/docs/content/tools/multicov.rst
index 64dd156eb4d7a382d6d1a6086ae809c1172e5f60..160461b920c254ae8de7358945e821589a93c444 100644
--- a/docs/content/tools/multicov.rst
+++ b/docs/content/tools/multicov.rst
@@ -1,3 +1,5 @@
+.. _multicov:
+
 ###############
 *multicov*
 ###############
@@ -93,4 +95,4 @@ command line.
    chr1	10000	20000	ivl2	123
    chr1	20000	30000	ivl3	213
    chr1	30000	40000	ivl4	335
-   
\ No newline at end of file
+   
diff --git a/docs/content/tools/multiinter.rst b/docs/content/tools/multiinter.rst
index 5578eec7b1d218a507e4cfb5c2e5f95f3965d993..87cbc6b64b9d8138792507038c051e4f6e7c2e6d 100644
--- a/docs/content/tools/multiinter.rst
+++ b/docs/content/tools/multiinter.rst
@@ -1,3 +1,5 @@
+.. _multiinter:
+
 ###############
 *multiinter*
-###############
\ No newline at end of file
+###############
diff --git a/docs/content/tools/nuc.rst b/docs/content/tools/nuc.rst
index 9daad02bab836040bf132e64f44fe40c216bb56d..fabe5757e16d45bc6b98d37d16ee22d59914dc43 100644
--- a/docs/content/tools/nuc.rst
+++ b/docs/content/tools/nuc.rst
@@ -1,3 +1,5 @@
+.. _nuc:
+
 ###############
 *nuc*
-###############
\ No newline at end of file
+###############
diff --git a/docs/content/tools/overlap.rst b/docs/content/tools/overlap.rst
index 6f7a2f57d2e49e41711d8ce09ce70ea2f9e6d47d..f365ead417fca98d0448b8459c69c2eb266e46c6 100755
--- a/docs/content/tools/overlap.rst
+++ b/docs/content/tools/overlap.rst
@@ -1,3 +1,5 @@
+.. _overlap:
+
 ###############
 *overlap*
 ###############
diff --git a/docs/content/tools/pairtobed.rst b/docs/content/tools/pairtobed.rst
index ceae68fb855e38f492110eb1b85aca53814a34cf..e872c9119b078ac35b47f332c9fb24a16bd703b0 100644
--- a/docs/content/tools/pairtobed.rst
+++ b/docs/content/tools/pairtobed.rst
@@ -1,3 +1,5 @@
+.. _pairtobed:
+
 ###############
 *pairtobed*
-###############
\ No newline at end of file
+###############
diff --git a/docs/content/tools/pairtopair.rst b/docs/content/tools/pairtopair.rst
index e286ec11b309d112d40248c8a5b691bec681e982..c4645a8f3b861fa5e40394f09b1a756ecf2ec98f 100755
--- a/docs/content/tools/pairtopair.rst
+++ b/docs/content/tools/pairtopair.rst
@@ -1,3 +1,5 @@
+.. _pairtopair:
+
 ###############
 *pairtopair*
 ###############
@@ -104,4 +106,4 @@ feature in B.
   
   Result              =====.................................=====
   
-  
\ No newline at end of file
+  
diff --git a/docs/content/tools/random.rst b/docs/content/tools/random.rst
index 7c3a3d399fa35abf41af2a3ad99ac6a906e2c5fc..680d1506bae70f50f6ba0ceb1a9852296df7a06f 100644
--- a/docs/content/tools/random.rst
+++ b/docs/content/tools/random.rst
@@ -1,3 +1,5 @@
+.. _random:
+
 ###############
 *random*
 ###############
diff --git a/docs/content/tools/reldist.rst b/docs/content/tools/reldist.rst
index b4a55a1496c1ff2a337bf01c92124093e52de3e9..c2698284b6b4acedbd8938c330191d3efdc99b7e 100644
--- a/docs/content/tools/reldist.rst
+++ b/docs/content/tools/reldist.rst
@@ -1,3 +1,5 @@
+.. _reldist:
+
 ###############
 *reldist*
 ###############
diff --git a/docs/content/tools/shuffle.rst b/docs/content/tools/shuffle.rst
index 0bde195463cc62eede860c1f7e219f614324f465..d846e5c24e2d82318009cebb894f64f150a63ce1 100755
--- a/docs/content/tools/shuffle.rst
+++ b/docs/content/tools/shuffle.rst
@@ -1,3 +1,5 @@
+.. _shuffle:
+
 ###############
 *shuffle*
 ###############
diff --git a/docs/content/tools/slop.rst b/docs/content/tools/slop.rst
index 1c1ea8df104b969acce1f04ab3614e8fc4bd6e95..fb4b9ae34eac8026531284aa56093c833b98b647 100755
--- a/docs/content/tools/slop.rst
+++ b/docs/content/tools/slop.rst
@@ -1,3 +1,5 @@
+.. _slop:
+
 ###############
 *slop*
 ###############
diff --git a/docs/content/tools/sort.rst b/docs/content/tools/sort.rst
index 24a01d16037da61d59926fbfe3a5a54fd37b2d65..05a4e3aac02297b44e9362a7f7443692d5473d44 100755
--- a/docs/content/tools/sort.rst
+++ b/docs/content/tools/sort.rst
@@ -1,3 +1,5 @@
+.. _sort:
+
 ###############
 *sort*
 ###############
diff --git a/docs/content/tools/subtract.rst b/docs/content/tools/subtract.rst
index 5c05be3036abaf4885170534f41a38998d2ec8eb..6b1d808258fe7c932a5043291d69727ead64a5dd 100755
--- a/docs/content/tools/subtract.rst
+++ b/docs/content/tools/subtract.rst
@@ -1,3 +1,5 @@
+.. _subtract:
+
 ###############
 *subtract*
 ###############
diff --git a/docs/content/tools/tag.rst b/docs/content/tools/tag.rst
index be6ad50698cf5e50959aa732170dc4c1828116f5..67930327195030abab79d8d336cd1daa504a724c 100644
--- a/docs/content/tools/tag.rst
+++ b/docs/content/tools/tag.rst
@@ -1,3 +1,5 @@
+.. _tag:
+
 ###############
 *tag*
-###############
\ No newline at end of file
+###############
diff --git a/docs/content/tools/unionbedg.rst b/docs/content/tools/unionbedg.rst
index 53819cedd94fc806d63d791d0a9985c79a8ae34f..1681324e00313cefd85bd99d07a7edf97a7be36f 100755
--- a/docs/content/tools/unionbedg.rst
+++ b/docs/content/tools/unionbedg.rst
@@ -1,3 +1,5 @@
+.. _unionbg:
+
 ###############
 *unionbedg*
 ###############
@@ -167,4 +169,4 @@ Figure:
   unionBedGraphs -i 1.snp.bg 2.snp.bg 3.snp.bg -filler -/-
   chr1 0 1 A/G C/C A/G
   chr1 5 6 C/T -/- C/T
-  chr1 7 8 -/- T/T -/-
\ No newline at end of file
+  chr1 7 8 -/- T/T -/-
diff --git a/docs/content/tools/window.rst b/docs/content/tools/window.rst
index 38dcfe07ade29c1942592d1fd74425dd80552b17..850180fc7dc6b2fcfa7879d14ff13bfcd2659b50 100755
--- a/docs/content/tools/window.rst
+++ b/docs/content/tools/window.rst
@@ -1,3 +1,5 @@
+.. _window:
+
 ###############
 *window*
 ###############