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commit: 348f9c5b9150fcbc7aac389c76e9ed702395c066 |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Sat Feb 25 19:15:53 2017 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Sat Feb 25 19:18:32 2017 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=348f9c5b |
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|
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sci-biology/cd-hit: Version bump to 4.6.6 |
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|
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Package-Manager: Portage-2.3.3, Repoman-2.3.1 |
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|
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sci-biology/cd-hit/Manifest | 1 + |
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sci-biology/cd-hit/cd-hit-4.6.6.ebuild | 48 +++++ |
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.../files/cd-hit-4.6.6-fix-build-system.patch | 122 ++++++++++++ |
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.../files/cd-hit-4.6.6-fix-perl-shebangs.patch | 219 +++++++++++++++++++++ |
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4 files changed, 390 insertions(+) |
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|
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diff --git a/sci-biology/cd-hit/Manifest b/sci-biology/cd-hit/Manifest |
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index 5d2ddfeed2..b671c47b32 100644 |
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--- a/sci-biology/cd-hit/Manifest |
21 |
+++ b/sci-biology/cd-hit/Manifest |
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@@ -1,3 +1,4 @@ |
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+DIST cd-hit-4.6.6.tar.gz 1152570 SHA256 97946f8ae62c3efa20ad4c527b8ea22200cf1b75c9941fb14de2bdaf1d6910f1 SHA512 8241d6674fb041559792dbbb58c12b41302d2275d3bacb1362946094b48a0b8e1236e71b5dc77d13405220b60f8253e6f996753a8b051995a72c8353d4333c51 WHIRLPOOL 4ee404e34a9c22aef0b809568aa1a7cefcd8d08e4a8c97d1c65b7692ae14b0567e5cc446054083219b56e89895117f69f786e6183f6c67d03d1f8404f7ba9632 |
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DIST cd-hit-v4.5.1-2011-01-31.tgz 368740 SHA256 c1c3a3a772fc683fec3ff1763fdeec62a0a2a3925124f7a723fe3b271da35281 SHA512 84beba384eb6e9bcf94c7e2ca63f862493fc0d058ad186752524a09016e01274229ca9b7a5275cd5454f54488235a6949e17090ffbf68ff441a613dbe5cf05a8 WHIRLPOOL 698d72f347b92091ade411bdbf540f4b4eeea6c742d3766e891bede7f1aa03024bd2f611a4235a6dec0ed9b9b5e06b3d69a7b8e6a7ab7d8139297b5a8b0da9d2 |
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DIST cd-hit-v4.5.4-2011-03-07.tgz 370264 SHA256 6de9074fada3c5f8109b670b8bdf96679dab45b841d36270d6c5e61a34284f6a SHA512 a093d15e26d6e226e5b37e43ed36affe58c0ee265bd43fd2098a39eafb54c7154ee1a7585da785324dc57532abe3401d48ad5a4a2de080fa6e1422091083683a WHIRLPOOL 3e2ea2db07ecc553d5f03f13a1092e85211257fb4a681629be0350d9cc3f3cc384d24bdb8b3e31d3f469fbc93070363afee608904b9ce3956ca24a8fa6d4d8e5 |
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DIST cd-hit-v4.6-2012-04-25.tgz 652228 SHA256 aa91e57bba61f04db39e83cdd6c8cdf082a006ea8c4c818b956b7531e4bcc2e9 SHA512 1004a4190643b6f5f1da067a4b911abc068d0bf7d909edd84f45d5fe9a1b17eb3276c0ddde391cbc5053a9ab979d09cbbe832615b7cce4fc2aeefce1d1bec52c WHIRLPOOL 1c7a50e40e9753c035a2920af09b024e9403f4a7cf1a801b998afd5b64189256857a236439f5b2935603fd4a691a722a9d74c3a373ab66c79faee9d8335834b4 |
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|
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diff --git a/sci-biology/cd-hit/cd-hit-4.6.6.ebuild b/sci-biology/cd-hit/cd-hit-4.6.6.ebuild |
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new file mode 100644 |
30 |
index 0000000000..49bea96899 |
31 |
--- /dev/null |
32 |
+++ b/sci-biology/cd-hit/cd-hit-4.6.6.ebuild |
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@@ -0,0 +1,48 @@ |
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+# Copyright 1999-2017 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+# $Id$ |
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+ |
38 |
+EAPI=6 |
39 |
+ |
40 |
+inherit flag-o-matic toolchain-funcs |
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+ |
42 |
+RELDATE="2016-0711" |
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+RELEASE="${PN}-v${PV}-${RELDATE}" |
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+ |
45 |
+DESCRIPTION="Clustering Database at High Identity with Tolerance" |
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+HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/" |
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+SRC_URI="https://github.com/weizhongli/cdhit/releases/download/V${PV}/${RELEASE}.tar.gz -> ${P}.tar.gz" |
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+ |
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+LICENSE="GPL-2" |
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+SLOT="0" |
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+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
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+IUSE="openmp" |
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+ |
54 |
+RDEPEND="dev-lang/perl" |
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+ |
56 |
+S="${WORKDIR}"/${RELEASE} |
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+ |
58 |
+PATCHES=( |
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+ "${FILESDIR}"/${PN}-4.6.6-fix-perl-shebangs.patch |
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+ "${FILESDIR}"/${PN}-4.6.6-fix-build-system.patch |
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+) |
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+ |
63 |
+pkg_pretend() { |
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+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp |
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+} |
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+ |
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+pkg_setup() { |
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+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp |
69 |
+} |
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+ |
71 |
+src_compile() { |
72 |
+ tc-export CXX |
73 |
+ emake openmp=$(usex openmp) |
74 |
+} |
75 |
+ |
76 |
+src_install() { |
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+ dodir /usr/bin |
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+ PREFIX="${EPREFIX}"/usr/bin default |
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+ |
80 |
+ dodoc doc/*.pdf |
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+} |
82 |
|
83 |
diff --git a/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-build-system.patch b/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-build-system.patch |
84 |
new file mode 100644 |
85 |
index 0000000000..c668d5c615 |
86 |
--- /dev/null |
87 |
+++ b/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-build-system.patch |
88 |
@@ -0,0 +1,122 @@ |
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+Fix build system, in order to honour user variables |
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+ |
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+--- a/makefile |
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++++ b/makefile |
93 |
+@@ -1,7 +1,4 @@ |
94 |
+- |
95 |
+-CC = g++ -Wall -ggdb |
96 |
+-CC = g++ -pg |
97 |
+-CC = g++ |
98 |
++CXX ?= g++ |
99 |
+ |
100 |
+ # without OpenMP |
101 |
+ |
102 |
+@@ -9,35 +6,19 @@ |
103 |
+ # in command line: |
104 |
+ # make openmp=yes |
105 |
+ ifeq ($(openmp),no) |
106 |
+- CCFLAGS = -DNO_OPENMP |
107 |
+-else |
108 |
+- CCFLAGS = -fopenmp |
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+-endif |
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+- |
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+-# support debugging |
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+-# in command line: |
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+-# make debug=yes |
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+-# make openmp=yes debug=yes |
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+-ifeq ($(debug),yes) |
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+-CCFLAGS += -ggdb |
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++ my_CPPFLAGS = -DNO_OPENMP |
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+ else |
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+-CCFLAGS += -O2 |
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++ my_CXXFLAGS = -fopenmp |
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+ endif |
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+ |
123 |
+ ifdef MAX_SEQ |
124 |
+-CCFLAGS += -DMAX_SEQ=$(MAX_SEQ) |
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++my_CPPFLAGS += -DMAX_SEQ=$(MAX_SEQ) |
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+ endif |
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+ |
128 |
+-#LDFLAGS = -static -o |
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+-LDFLAGS += -o |
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+- |
131 |
+ PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454 |
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+ |
133 |
+-# Propagate hardening flags |
134 |
+-CCFLAGS := $(CPPFLAGS) $(CCFLAGS) $(CXXFLAGS) |
135 |
+- |
136 |
+ .c++.o: |
137 |
+- $(CC) $(CCFLAGS) -c $< |
138 |
++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $< |
139 |
+ |
140 |
+ all: $(PROGS) |
141 |
+ |
142 |
+@@ -47,52 +28,52 @@ |
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+ # programs |
144 |
+ |
145 |
+ cd-hit: cdhit-common.o cdhit-utility.o cdhit.o |
146 |
+- $(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit |
147 |
++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit.o cdhit-common.o cdhit-utility.o -o cd-hit |
148 |
+ |
149 |
+ cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o |
150 |
+- $(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d |
151 |
++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-2d |
152 |
+ |
153 |
+ cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o |
154 |
+- $(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est |
155 |
++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o -o cd-hit-est |
156 |
+ |
157 |
+ cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o |
158 |
+- $(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d |
159 |
++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-est-2d |
160 |
+ |
161 |
+ cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o |
162 |
+- $(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div |
163 |
++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o -o cd-hit-div |
164 |
+ |
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+ cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o |
166 |
+- $(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454 |
167 |
++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o -o cd-hit-454 |
168 |
+ |
169 |
+ # objects |
170 |
+ cdhit-common.o: cdhit-common.c++ cdhit-common.h |
171 |
+- $(CC) $(CCFLAGS) cdhit-common.c++ -c |
172 |
++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-common.c++ -c |
173 |
+ |
174 |
+ cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h |
175 |
+- $(CC) $(CCFLAGS) cdhit-utility.c++ -c |
176 |
++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-utility.c++ -c |
177 |
+ |
178 |
+ cdhit.o: cdhit.c++ cdhit-utility.h |
179 |
+- $(CC) $(CCFLAGS) cdhit.c++ -c |
180 |
++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit.c++ -c |
181 |
+ |
182 |
+ cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h |
183 |
+- $(CC) $(CCFLAGS) cdhit-2d.c++ -c |
184 |
++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-2d.c++ -c |
185 |
+ |
186 |
+ cdhit-est.o: cdhit-est.c++ cdhit-utility.h |
187 |
+- $(CC) $(CCFLAGS) cdhit-est.c++ -c |
188 |
++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-est.c++ -c |
189 |
+ |
190 |
+ cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h |
191 |
+- $(CC) $(CCFLAGS) cdhit-est-2d.c++ -c |
192 |
++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-est-2d.c++ -c |
193 |
+ |
194 |
+ cdhit-div.o: cdhit-div.c++ cdhit-common.h |
195 |
+- $(CC) $(CCFLAGS) cdhit-div.c++ -c |
196 |
++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-div.c++ -c |
197 |
+ |
198 |
+ cdhit-454.o: cdhit-454.c++ cdhit-common.h |
199 |
+- $(CC) $(CCFLAGS) cdhit-454.c++ -c |
200 |
++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-454.c++ -c |
201 |
+ |
202 |
+ PREFIX ?= /usr/local/bin |
203 |
+ |
204 |
+ install: |
205 |
+ for prog in $(PROGS); do \ |
206 |
+- install -m 0755 $$prog $(PREFIX); \ |
207 |
++ install -m 0755 $$prog $(DESTDIR)$(PREFIX); \ |
208 |
+ done |
209 |
+- install -m 0755 *.pl $(PREFIX); |
210 |
++ install -m 0755 *.pl $(DESTDIR)$(PREFIX); |
211 |
|
212 |
diff --git a/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-perl-shebangs.patch b/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-perl-shebangs.patch |
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new file mode 100644 |
214 |
index 0000000000..3784296f2e |
215 |
--- /dev/null |
216 |
+++ b/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-perl-shebangs.patch |
217 |
@@ -0,0 +1,219 @@ |
218 |
+Make perl shebangs more Prefix friendly |
219 |
+See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/ |
220 |
+ |
221 |
+--- a/cd-hit-2d-para.pl |
222 |
++++ b/cd-hit-2d-para.pl |
223 |
+@@ -1,4 +1,4 @@ |
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+-#!/usr/bin/perl -w |
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++#!/usr/bin/env perl |
226 |
+ # ============================================================================= |
227 |
+ # CD-HIT |
228 |
+ # http://cd-hit.org/ |
229 |
+--- a/cd-hit-div.pl |
230 |
++++ b/cd-hit-div.pl |
231 |
+@@ -1,4 +1,4 @@ |
232 |
+-#!/usr/bin/perl |
233 |
++#!/usr/bin/env perl |
234 |
+ |
235 |
+ #not like cd-hit-div, this script do not sort input |
236 |
+ #or throw away seq |
237 |
+--- a/cd-hit-para.pl |
238 |
++++ b/cd-hit-para.pl |
239 |
+@@ -1,4 +1,4 @@ |
240 |
+-#!/usr/bin/perl -w |
241 |
++#!/usr/bin/env perl |
242 |
+ # ============================================================================= |
243 |
+ # CD-HIT |
244 |
+ # http://cd-hit.org/ |
245 |
+--- a/clstr2tree.pl |
246 |
++++ b/clstr2tree.pl |
247 |
+@@ -1,4 +1,4 @@ |
248 |
+-#!/usr/bin/perl |
249 |
++#!/usr/bin/env perl |
250 |
+ |
251 |
+ $clstr = shift; |
252 |
+ $fr = shift; # for nr80.clstr $fr = 0.8 |
253 |
+--- a/clstr2txt.pl |
254 |
++++ b/clstr2txt.pl |
255 |
+@@ -1,4 +1,4 @@ |
256 |
+-#!/usr/bin/perl |
257 |
++#!/usr/bin/env perl |
258 |
+ |
259 |
+ my $no = 0; |
260 |
+ my $clstr_no = ""; |
261 |
+--- a/clstr2xml.pl |
262 |
++++ b/clstr2xml.pl |
263 |
+@@ -1,4 +1,4 @@ |
264 |
+-#!/usr/bin/perl |
265 |
++#!/usr/bin/env perl |
266 |
+ |
267 |
+ #usage: clstr_xml.pl [-len|-size] level1.clstr [level2.clstr level3.clstr ...] |
268 |
+ #purpose: to create xml file from cd-hit or hierarchical cd-hit(h-cd-hit) results |
269 |
+--- a/clstr_cut.pl |
270 |
++++ b/clstr_cut.pl |
271 |
+@@ -1,4 +1,4 @@ |
272 |
+-#!/usr/bin/perl |
273 |
++#!/usr/bin/env perl |
274 |
+ |
275 |
+ #keep only top $no proteins in cluster |
276 |
+ |
277 |
+--- a/clstr_merge_noorder.pl |
278 |
++++ b/clstr_merge_noorder.pl |
279 |
+@@ -1,4 +1,4 @@ |
280 |
+-#!/usr/bin/perl |
281 |
++#!/usr/bin/env perl |
282 |
+ |
283 |
+ # order of clusters don't need to be the same |
284 |
+ # but then I have to read everything into memory |
285 |
+--- a/clstr_merge.pl |
286 |
++++ b/clstr_merge.pl |
287 |
+@@ -1,4 +1,4 @@ |
288 |
+-#!/usr/bin/perl |
289 |
++#!/usr/bin/env perl |
290 |
+ |
291 |
+ # the order of clusters need to be identical |
292 |
+ my ($master_clstr, @clstr) = @ARGV; |
293 |
+--- a/clstr_quality_eval_by_link.pl |
294 |
++++ b/clstr_quality_eval_by_link.pl |
295 |
+@@ -1,4 +1,4 @@ |
296 |
+-#!/usr/bin/perl |
297 |
++#!/usr/bin/env perl |
298 |
+ |
299 |
+ ## calculate the sensitivity and specificity of clusters |
300 |
+ ## if the input fasta file has pre-defined classification term |
301 |
+--- a/clstr_quality_eval.pl |
302 |
++++ b/clstr_quality_eval.pl |
303 |
+@@ -1,4 +1,4 @@ |
304 |
+-#!/usr/bin/perl |
305 |
++#!/usr/bin/env perl |
306 |
+ |
307 |
+ ## calculate the sensitivity and specificity of clusters |
308 |
+ ## if the input fasta file has pre-defined classification term |
309 |
+--- a/clstr_reduce.pl |
310 |
++++ b/clstr_reduce.pl |
311 |
+@@ -1,4 +1,4 @@ |
312 |
+-#!/usr/bin/perl |
313 |
++#!/usr/bin/env perl |
314 |
+ |
315 |
+ |
316 |
+ $file90 = shift; |
317 |
+--- a/clstr_renumber.pl |
318 |
++++ b/clstr_renumber.pl |
319 |
+@@ -1,4 +1,4 @@ |
320 |
+-#!/usr/bin/perl |
321 |
++#!/usr/bin/env perl |
322 |
+ $no = 0; |
323 |
+ while($ll=<>){ |
324 |
+ if ($ll =~ /^>Cluster (\d+)/) { |
325 |
+--- a/clstr_rep.pl |
326 |
++++ b/clstr_rep.pl |
327 |
+@@ -1,4 +1,4 @@ |
328 |
+-#!/usr/bin/perl |
329 |
++#!/usr/bin/env perl |
330 |
+ |
331 |
+ $rep = ""; |
332 |
+ $no = 0; |
333 |
+--- a/clstr_reps_faa_rev.pl |
334 |
++++ b/clstr_reps_faa_rev.pl |
335 |
+@@ -1,4 +1,4 @@ |
336 |
+-#!/usr/bin/perl |
337 |
++#!/usr/bin/env perl |
338 |
+ # output single fasta file |
339 |
+ # for each cluster output at least $cutoff seqs |
340 |
+ |
341 |
+--- a/clstr_rev.pl |
342 |
++++ b/clstr_rev.pl |
343 |
+@@ -1,4 +1,4 @@ |
344 |
+-#!/usr/bin/perl |
345 |
++#!/usr/bin/env perl |
346 |
+ # if nr90 from nr100 and |
347 |
+ # nr80 from nr90, so I have nr90.clstr and nr80.clstr |
348 |
+ # but, in nr80.clstr, some gi numbers whose from nr100 are there |
349 |
+--- a/clstr_select.pl |
350 |
++++ b/clstr_select.pl |
351 |
+@@ -1,4 +1,4 @@ |
352 |
+-#!/usr/bin/perl |
353 |
++#!/usr/bin/env perl |
354 |
+ |
355 |
+ #my $by = shift; |
356 |
+ my $min; |
357 |
+--- a/clstr_select_rep.pl |
358 |
++++ b/clstr_select_rep.pl |
359 |
+@@ -1,4 +1,4 @@ |
360 |
+-#!/usr/bin/perl |
361 |
++#!/usr/bin/env perl |
362 |
+ |
363 |
+ #my $by = shift; |
364 |
+ my $min; |
365 |
+--- a/clstr_size_histogram.pl |
366 |
++++ b/clstr_size_histogram.pl |
367 |
+@@ -1,4 +1,4 @@ |
368 |
+-#!/usr/bin/perl |
369 |
++#!/usr/bin/env perl |
370 |
+ |
371 |
+ if(@ARGV==0){ |
372 |
+ print "Usage:\n\tclstr_size_histogram.pl [-bin N] clstr_file\n"; |
373 |
+--- a/clstr_size_stat.pl |
374 |
++++ b/clstr_size_stat.pl |
375 |
+@@ -1,4 +1,4 @@ |
376 |
+-#!/usr/bin/perl |
377 |
++#!/usr/bin/env perl |
378 |
+ |
379 |
+ if(@ARGV==0){ |
380 |
+ print "Usage:\n\tclstr_size_stat.pl clstr_file\n"; |
381 |
+--- a/clstr_sort_by.pl |
382 |
++++ b/clstr_sort_by.pl |
383 |
+@@ -1,4 +1,4 @@ |
384 |
+-#!/usr/bin/perl |
385 |
++#!/usr/bin/env perl |
386 |
+ |
387 |
+ my $sort_by_what = shift; |
388 |
+ $sort_by_what = "no" unless $sort_by_what; |
389 |
+--- a/clstr_sort_prot_by.pl |
390 |
++++ b/clstr_sort_prot_by.pl |
391 |
+@@ -1,4 +1,4 @@ |
392 |
+-#!/usr/bin/perl |
393 |
++#!/usr/bin/env perl |
394 |
+ |
395 |
+ my $sort_by = shift; |
396 |
+ $sort_by = "len" unless ($sort_by); |
397 |
+--- a/clstr_sql_tbl.pl |
398 |
++++ b/clstr_sql_tbl.pl |
399 |
+@@ -1,4 +1,4 @@ |
400 |
+-#!/usr/bin/perl |
401 |
++#!/usr/bin/env perl |
402 |
+ |
403 |
+ if(@ARGV==0){ |
404 |
+ print "Usage:\n\tclstr_sql_tbl.pl clstr_file tbl_file\n"; |
405 |
+--- a/clstr_sql_tbl_sort.pl |
406 |
++++ b/clstr_sql_tbl_sort.pl |
407 |
+@@ -1,4 +1,4 @@ |
408 |
+-#!/usr/bin/perl |
409 |
++#!/usr/bin/env perl |
410 |
+ |
411 |
+ if(@ARGV==0){ |
412 |
+ print "Usage:\n\tclstr_sql_tbl_sort.pl table_file level\n"; |
413 |
+--- a/make_multi_seq.pl |
414 |
++++ b/make_multi_seq.pl |
415 |
+@@ -1,4 +1,4 @@ |
416 |
+-#!/usr/bin/perl |
417 |
++#!/usr/bin/env perl |
418 |
+ |
419 |
+ #note you have to use "-d 0" in the cd-hit run |
420 |
+ #note you better to use "-g 1" in the cd-hit run |
421 |
+--- a/plot_2d.pl |
422 |
++++ b/plot_2d.pl |
423 |
+@@ -1,4 +1,4 @@ |
424 |
+-#!/usr/bin/perl |
425 |
++#!/usr/bin/env perl |
426 |
+ |
427 |
+ use Image::Magick; |
428 |
+ |
429 |
+--- a/plot_len1.pl |
430 |
++++ b/plot_len1.pl |
431 |
+@@ -1,4 +1,4 @@ |
432 |
+-#!/usr/bin/perl |
433 |
++#!/usr/bin/env perl |
434 |
+ |
435 |
+ $file90 = shift; |
436 |
+ $segs = shift; |