[med-svn] [infernal] 02/08: SVN-Git conversion failed - just commit status of 1.0.2 (oldstable at the time of conversion)

Andreas Tille tille at debian.org
Tue Jun 21 09:28:59 UTC 2016


This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository infernal.

commit d0c0d54ab7239a160d1974d789049b49871b9547
Author: Andreas Tille <tille at debian.org>
Date:   Tue Jun 21 11:19:17 2016 +0200

    SVN-Git conversion failed - just commit status of 1.0.2 (oldstable at the time of conversion)
---
 debian/README.Debian                 |  29 +++++++
 debian/README.source                 |  23 ++++++
 debian/changelog                     |  67 ++++++++++++++++
 debian/compat                        |   1 +
 debian/control                       |  55 ++++++++++++++
 debian/copyright                     | 143 +++++++++++++++++++++++++++++++++++
 debian/infernal-doc.doc-base         |  16 ++++
 debian/infernal-doc.install          |   1 +
 debian/infernal.docs                 |   3 +
 debian/infernal.install              |   9 +++
 debian/infernal.manpages             |   1 +
 debian/patches/format_security.patch |  41 ++++++++++
 debian/patches/series                |   1 +
 debian/rules                         |  26 +++++++
 debian/upstream-metadata.yaml        |  14 ++++
 debian/watch                         |   3 +
 16 files changed, 433 insertions(+)

diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..e38f635
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,29 @@
+infernal for Debian
+-------------------
+
+The documentation for easel contains many PDFs that are not buildable
+from source - although Debian most likely provide the tools at least to
+prepare some of the figures, e.g., a sequence alignment.  Other figures
+would be more difficult to prepare. As an interim solution it was decided
+to leave that documentation out and users are requested to address the
+web pages of the upstream developers in this matter.
+
+The directory "squid" that is distributed with the source of infernal
+differs slightly from the biosquid Debian package. Upstream was contacted
+about this redundancy to his own software and the answer was to please
+leave with that situation since the two are not safely substituted for
+another.
+
+Infernal offers to be compiled for LAM-MPI. Please contact us if there is
+respective demand. Also, the Large File Support (LFS) was not activated,
+which may be of concern for large screening projects on files larger
+than 2GB.
+
+Infernal optionally uses the CFSQP library which is non-free. This is
+not supported by this Debian package. Please address the Userguide for
+instructions of a manual self-compilation and -installation.
+
+The packaging has become part of the Debian Med Blend
+and everyone interested is invited to join in for maintaining it.
+
+ -- Steffen Moeller <moeller at debian.org>  Mon, 10 Sep 2007 23:15:37 +0200
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..e481526
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,23 @@
+infernal - Changes to upstream source distribution
+==================================================
+
+Upstream provides a readily readable userguide
+for Infernal, which is also available online at
+ftp://selab.janelia.org/pub/software/infernal/Userguide.pdf
+and should better not be distributed with the source to 
+save disk space.
+
+The PDFs that are coming with the sources from which
+the userguide is built are indeed upstream's original
+sources. They are edited with a PDF editor. Upstream,
+Dr Eddy, was consulted in this issue.
+
+Some figures like the sequence alignments could be prepared
+with the infrastructure that Debian provides and thus would
+not be ultimately required to be shipped as PDFs. This is however
+tolerated.
+
+The redundancy of the squid folder with the Debian package
+biosquid needs to remain until upstream resolves the conflicts.
+
+-- Steffen Moeller   Sun, 20 Jan 2008 23:05:22 +0100
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..0b42af0
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,67 @@
+infernal (1.0.2-2) unstable; urgency=low
+
+  * Series of mall fixes (Closes: #643407).
+  * source/format 3.0
+  * Policy to 3.9.2
+  * added infernal-dbg
+  * corrected upstream's email address
+
+ -- Steffen Moeller <moeller at debian.org>  Tue, 27 Sep 2011 15:48:27 +0200
+
+infernal (1.0.2-1) unstable; urgency=low
+
+  * New upstream version
+
+ -- Andreas Tille <tille at debian.org>  Tue, 03 Nov 2009 11:15:34 +0100
+
+infernal (1.0-2) unstable; urgency=low
+
+  * Switch to CDBS to benefit from automagical config.{sub,guess}
+    update (debian/rules). Closes: #550253.
+  * debian/control:
+    - Depend on cdbs, downgraded requirement on debhelper from 7.1 to 7.
+    - Transferred bibliographic information from the package description
+      to debian/upstream-metadata.yaml.
+    - Clarified the short description of the documentation package.
+  * Removed debian/infernal.dirs, not needed.
+  * Edited README.source, removing mention that infernal is in contrib.
+  * debian/copyright points at the version 3 of the GPL.
+
+ -- Charles Plessy <plessy at debian.org>  Sat, 10 Oct 2009 11:22:35 +0900
+
+infernal (1.0-1) unstable; urgency=low
+
+  [ Charles Plessy ]
+  * Updated my email address.
+
+  [ Andreas Tille ]
+  * New upstream version
+  * debian/control:
+    - Standards-Version: 3.8.3 (no changes needed)
+    - Added myself to uploaders
+    - s/Debian-Med/Debian Med/
+    - Build-Depends: debhelper (>= 7.1) autotools-dev
+    - Package: infernal-doc
+  * debian/rules rewritten to make use of short dh
+  * debian/copyright:
+    - added myself to Copyright holders of debian/*
+    - squid is not part of the upstream tarball anymore so this
+      paragraph was deleted
+    - files/Userguide.pdf: Copied comment about PDF = source from
+      README.Debian
+  * debian/infernal-doc.doc-base
+  * debian/infernal.install: install src/{trcyk,truncyk_check} to
+    /usr/bin
+
+  * TODO: Convince upstream to release libeazel which is also used in
+    hmmer as a separate library instead of copying the code into
+    different projects
+
+ -- Andreas Tille <tille at debian.org>  Fri, 25 Sep 2009 15:17:22 +0200
+
+infernal (0.81-1) experimental; urgency=low
+
+  * Initial release (Closes: #441840)
+
+ -- Steffen Moeller <moeller at debian.org>  Mon, 10 Sep 2007 23:15:37 +0200
+
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..7f8f011
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+7
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..a574be8
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,55 @@
+Source: infernal
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Charles Plessy <plessy at debian.org>,
+ Andreas Tille <tille at debian.org>
+Build-Depends: cdbs, debhelper (>= 7), autotools-dev, quilt
+Standards-Version: 3.9.2
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/infernal/trunk/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/infernal/trunk/
+Homepage: http://infernal.janelia.org/
+
+Package: infernal
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: inference of RNA secondary structural alignments
+ Infernal ("INFERence of RNA ALignment") is for searching DNA sequence
+ databases for RNA structure and sequence similarities. It is an
+ implementation of a special case of profile stochastic context-free
+ grammars called covariance models (CMs). A CM is like a sequence
+ profile, but it scores a combination of sequence consensus and RNA
+ secondary structure consensus, so in many cases, it is more capable of
+ identifying RNA homologs that conserve their secondary structure more
+ than their primary sequence.
+ .
+ The tool is an integral component of the Rfam database.
+
+Package: infernal-doc
+Architecture: all
+Section: doc
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: inference of RNA secondary structural alignments – documentation
+ Infernal ("INFERence of RNA ALignment") is for searching DNA sequence
+ databases for RNA structure and sequence similarities. It is an
+ implementation of a special case of profile stochastic context-free
+ grammars called covariance models (CMs). A CM is like a sequence
+ profile, but it scores a combination of sequence consensus and RNA
+ secondary structure consensus, so in many cases, it is more capable of
+ identifying RNA homologs that conserve their secondary structure more
+ than their primary sequence.
+ .
+ This package provides the documentation which is shipped with the
+ code of infernal.
+
+Package: infernal-dbg
+Architecture: any
+Section: debug
+Depends: ${misc:Depends}, infernal (= ${binary:Version})
+Description: debug information for infernal
+ This package contains extra information to help the debugging of the
+ infernal suite. The package is auto-generated. You may be asked
+ by the upstream developer to install it to help the identification
+ of a technical problem.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..ec11dbc
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,143 @@
+X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+X-Debianized-By: Steffen Moeller <moeller at debian.org>
+X-Debianized-Date: Mon, 10 Sep 2007 23:15:37 +0200
+X-Source-Downloaded-From: ftp://infernal.janelia.org/pub/software/infernal
+X-Upstream-Author: Infernal developer team at HHMI Janelia Farm:
+			Diana Kolbe <kolbed janelia.hhmi.org>
+			Eric Nawrocki <nawrockie janelia.hhmi.org>
+			Sean Eddy <eddys janelia.hhmi.org>.
+                   The "rigfilters" code was contributed by Zasha Weinberg
+		   and Larry Ruzzo, University of Washington, Seattle.
+
+
+Files: debian/*
+Copyright: © 2007-2008 Steffen Moeller <moeller at debian.org>
+           © 2007-2008 Charles Plessy <plessy at debian.org>
+           © 2009 Andreas Tille <tille at debian.org>
+License: Same as infernal
+
+Files: rigfilters/*
+Copyright: © 2004, Zasha Weinberg
+License: BSD family
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ .
+ - Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+ - Redistributions in binary form must reproduce the above
+   copyright notice, this list of conditions and the following
+   disclaimer in the documentation and/or other materials provided
+   with the distribution.
+ - Neither the name of the University of Washington nor the names of
+   its contributors may be used to endorse or promote products derived
+   from this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+ NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+ FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT
+ SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
+ IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Files: easel/{esl_sse.c,esl_vmx.c}
+Copyright: © 2007 Julien Pommier
+           © 1992 Stephen Moshier
+License: BSD
+
+Files: easel/easel.c::esl_tmpfile()
+Copyright: © 1999-2001 David A. Wheeler
+License: MIT
+
+Files: easel/esl_regexp.c
+Copyright: © 1986, 1993, 1995 by University of Toronto
+License: BSD
+
+Files: easel/*
+Copyright: © 2004-2008 Sean R. Eddy
+           © 2006-2008 Howard Hughes Medical Institute
+License: Easel - a library of C functions for biological sequence analysis
+ @EASEL_COPYRIGHT@
+ .
+ The Easel library is freely modifiable and redistributable under the
+ Janelia Farm Software License, a BSD license:
+ .
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are
+ met:
+ .
+ 1. Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+ .
+ 2. Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in
+    the documentation and/or other materials provided with the
+    distribution.
+ .
+ 3. Neither the name of the Howard Hughes Medical Institute nor the
+    names of its contributors may be used to endorse or promote
+    products derived from this software without specific prior written
+    permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, ANY IMPLIED WARRANTIES OF MERCHANTABILITY,
+ NON-INFRINGEMENT, OR FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+ REASONABLE ROYALTIES; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
+ TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
+ USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+ DAMAGE.
+
+
+Files: Userguide.pdf
+X-Comment: The PDFs that are coming with the sources from which the userguide is
+ built are indeed upstream's original sources. They are edited with a PDF
+ editor. Upstream, Dr Eddy, was consulted in this issue.
+
+
+Files: *
+Copyright: © 2001-2007 HHMI Janelia Farm
+           © 1991-2007      Sean R. Eddy
+           © 2005-2007      Eric P. Nawrocki
+           © 2005-2007      Diana L. Kolbe
+           © 2004           Zasha Weinberg
+           © 1990           Don G. Gilbert
+           © 1995-2006      Washington University in St. Louis
+           © 1992-1995      Medical Research Council, UK
+           © 2004           University of Washington, Seattle
+           © 1986,1993,1995 University of Toronto
+           © 1989-2001      Free Software Foundation
+           © 1991           Massachusetts Institute of Technology
+License: GPL-3
+ This suite of programs is free software. You can redistribute it
+ and/or modify it under the terms of the GNU General Public License as
+ published by the Free Software Foundation; either version 2 of the
+ License, or (at your option) any later version.
+ .
+ In other words, you may modify, copy, or redistribute this source code
+ and its documentation, but if you do, you must preserve all these
+ copyrights and distribute all derivative versions as free software
+ under the GNU General Public License.
+ .
+ This software is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this software, in the file LICENSE; if not, write to the
+ Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston,
+ MA 02110-1301, USA or see http://www.gnu.org/
+X-Comment: On Debian systems, the complete text of the GNU General Public
+ License version 3 can be found in `/usr/share/common-licenses/GPL-3'.
diff --git a/debian/infernal-doc.doc-base b/debian/infernal-doc.doc-base
new file mode 100644
index 0000000..46da2d3
--- /dev/null
+++ b/debian/infernal-doc.doc-base
@@ -0,0 +1,16 @@
+Document: infernal-doc
+Title: INFERNAL User’s Guide
+Author: Diana Kolbe, Eric Nawrocki, Sean Eddy
+Abstract: Sequence analysis using profiles of RNA secondary structure consensus
+ Infernal ("INFERence of RNA ALignment") is for searching DNA sequence
+ databases for RNA structure and sequence similarities. It is an
+ implementation of a special case of profile stochastic context-free
+ grammars called covariance models (CMs). A CM is like a sequence
+ profile, but it scores a combination of sequence consensus and RNA
+ secondary structure consensus, so in many cases, it is more capable of
+ identifying RNA homologs that conserve their secondary structure more
+ than their primary sequence.
+Section: Science/Biology
+
+Format: pdf
+Files: /usr/share/doc/infernal/Userguide.pdf
diff --git a/debian/infernal-doc.install b/debian/infernal-doc.install
new file mode 100644
index 0000000..5fec2fd
--- /dev/null
+++ b/debian/infernal-doc.install
@@ -0,0 +1 @@
+Userguide.pdf   usr/share/doc/infernal
diff --git a/debian/infernal.docs b/debian/infernal.docs
new file mode 100644
index 0000000..5d21f8a
--- /dev/null
+++ b/debian/infernal.docs
@@ -0,0 +1,3 @@
+00README
+00README-MPI
+documentation/release-notes/RELEASE-1.0
diff --git a/debian/infernal.install b/debian/infernal.install
new file mode 100644
index 0000000..52bcea9
--- /dev/null
+++ b/debian/infernal.install
@@ -0,0 +1,9 @@
+src/cmalign       usr/bin
+src/cmbuild       usr/bin
+src/cmcalibrate   usr/bin
+src/cmemit        usr/bin
+src/cmscore       usr/bin
+src/cmsearch      usr/bin
+src/cmstat        usr/bin
+src/trcyk         usr/bin
+src/truncyk_check usr/bin
diff --git a/debian/infernal.manpages b/debian/infernal.manpages
new file mode 100644
index 0000000..72c3bba
--- /dev/null
+++ b/debian/infernal.manpages
@@ -0,0 +1 @@
+documentation/manpages/*
diff --git a/debian/patches/format_security.patch b/debian/patches/format_security.patch
new file mode 100644
index 0000000..b1a0da3
--- /dev/null
+++ b/debian/patches/format_security.patch
@@ -0,0 +1,41 @@
+Index: infernal-1.0.2/easel/esl_getopts.c
+===================================================================
+--- infernal-1.0.2.orig/easel/esl_getopts.c	2009-10-30 18:30:58.000000000 +0100
++++ infernal-1.0.2/easel/esl_getopts.c	2011-09-27 15:52:41.490289335 +0200
+@@ -1270,7 +1270,7 @@
+ 		   "Arg looks like option? Use %.24s%.24s if you really mean it.",
+ 		   g->opt[opti].name, *ret_optarg);
+       } else 
+-	ESL_FAIL(eslESYNTAX, "Option %.24s requires an argument", g->opt[opti].name);
++	ESL_FAIL(eslESYNTAX, g->errbuf, "Option %.24s requires an argument", g->opt[opti].name);
+ 
+       g->optstring = NULL;   /* An optchar that takes an arg must terminate an optstring. */
+     }
+Index: infernal-1.0.2/easel/esl_msa.c
+===================================================================
+--- infernal-1.0.2.orig/easel/esl_msa.c	2009-10-30 18:30:55.000000000 +0100
++++ infernal-1.0.2/easel/esl_msa.c	2011-09-27 15:57:44.961318373 +0200
+@@ -3614,7 +3614,8 @@
+   ESL_MSA     *msa         = NULL;
+ 
+   if (esl_tmpfile_named(tmpfile, &fp)            != eslOK) goto ERROR;
+-  fprintf(fp, s);
++  //fprintf(fp, s); // provokes error: format not a string literal and no format arguments [-Werror=format-security]
++  fputs(s,fp);
+   fclose(fp); 
+   fp = NULL;
+   if (esl_msafile_Open(tmpfile, fmt, NULL, &mfp) != eslOK) goto ERROR;
+Index: infernal-1.0.2/easel/esl_tree.c
+===================================================================
+--- infernal-1.0.2.orig/easel/esl_tree.c	2009-10-30 18:30:58.000000000 +0100
++++ infernal-1.0.2/easel/esl_tree.c	2011-09-27 15:59:14.101032221 +0200
+@@ -149,7 +149,8 @@
+   ESL_TREE *T           = NULL;
+ 
+   if (esl_tmpfile(tmpfile, &fp)         != eslOK) goto ERROR;
+-  fprintf(fp, s);
++  //fprintf(fp, s); // provokes error: format not a string literal and no format arguments [-Werror=format-security]
++  fputs(s,fp);
+   rewind(fp);
+   if (esl_tree_ReadNewick(fp, NULL, &T) != eslOK) goto ERROR;
+   fclose(fp);
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..3360a11
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+format_security.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..4a98d4d
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,26 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+%:
+	dh  $@ --with quilt
+
+override_dh_auto_clean:
+	if [ -r Makefile ]; then $(MAKE) distclean; fi
+	cd documentation/userguide; make distclean
+	cd easel/documentation; make distclean
+	dh_clean *.1 */*.log *.log */Makefile Makefile documentation/manpages/*.1
+
+override_dh_compress :
+	dh_compress -X.pdf
+
+override_dh_strip:
+	dh_strip --dbg-package=infernal-dbg
+
+
+override_dh_auto_install:
+	$(MAKE) install prefix=$(CURDIR)/debian/tmp
+
+get-orig-source:
+	VERSION=`dpkg-parsechangelog | grep Ver | cut -d' ' -f2 | cut -d- -f1` ; \
+	URL="ftp://selab.janelia.org/pub/software/infernal/infernal-$${VERSION}.tar.gz"; \
+	ln -s infernal-$${VERSION}.tar.gz infernal_$${VERSION}.orig.tar.gz
diff --git a/debian/upstream-metadata.yaml b/debian/upstream-metadata.yaml
new file mode 100644
index 0000000..824dc07
--- /dev/null
+++ b/debian/upstream-metadata.yaml
@@ -0,0 +1,14 @@
+DOI: 10.1093/bioinformatics/btp157
+Homepage: http://infernal.janelia.org/
+PMID: 19307242
+Reference: 
+ author: Nawrocki, Eric P. and Kolbe, Diana L. and Eddy, Sean R.
+ title: Infernal 1.0: inference of RNA alignments
+ journal: Bioinformatics
+ volume: 25
+ number: 10
+ pages: 1335-1337
+ doi: 10.1093/bioinformatics/btp157
+ year: 2009
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/10/1335
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/25/10/1335.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..0957a47
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+opts="passive,uversionmangle=s/(rc\d+)/~$1/" \
+  ftp://infernal.janelia.org/pub/software/infernal/infernal-(.*)\.tar\.gz

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