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Build instructions for hydra: structural variation detection

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1 parent a8506ac commit 5279ceb6aa93a67b8615db656cc9742e64c266a7 @chapmanb chapmanb committed Jan 24, 2012
Showing with 14 additions and 1 deletion.
  1. +10 −0 cloudbio/custom/bio_nextgen.py
  2. +2 −1 cloudbio/custom/shared.py
  3. +2 −0 config/custom.yaml
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10 cloudbio/custom/bio_nextgen.py
@@ -386,3 +386,13 @@ def install_macs(env):
url = "http://macs:chipseq@liulab.dfci.harvard.edu/MACS/src/" \
"MACS-%s.tar.gz" % version
_get_install(url, env, _python_make)
+
+# --- Structural variation
+@_if_not_installed("hydra")
+def install_hydra(env):
+ version = "0.5.3"
+ url = "http://hydra-sv.googlecode.com/files/Hydra.v{}.tar.gz".format(version)
+ def clean_libs(env):
+ run("make clean")
+ _get_install(url, env, _make_copy("ls -1 bin/* scripts/*"),
+ post_unpack_fn=clean_libs)
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3 cloudbio/custom/shared.py
@@ -70,7 +70,8 @@ def _safe_dir_name(dir_name, need_dir=True):
return check
# still couldn't find it, it's a nasty one
for check_part in (dir_name.split("-")[0].split("_")[0],
- dir_name.split("-")[-1].split("_")[-1]):
+ dir_name.split("-")[-1].split("_")[-1],
+ dir_name.split(".")[0]):
with settings(hide('warnings', 'running', 'stdout', 'stderr'),
warn_only=True):
dirs = run("ls -d1 *%s*/" % check_part).split("\n")
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2 config/custom.yaml
@@ -36,6 +36,8 @@ bio_nextgen:
- transabyss
- trinity
- velvet
+ sv:
+ - hydra
chip:
- macs
needs_64bit:

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