New upstream version 1.1.3

configure

easel

hmmer

 No newline at end of file

Brief installation instructions 

Infernal 1.1.2; July 2016

Infernal 1.1.3; Nov 2019

-------------------------------------------------------------

These are quick installation instructions. For complete documentation,

including customization and troubleshooting, please see the

Installation chapter in the Infernal User's Guide (Userguide.pdf).

Starting from a source distribution, infernal-1.1.2.tar.gz:

 uncompress:                uncompress infernal-1.1.2.tar.gz  

 unpack:                    tar xf infernal-1.1.2.tar

 move into new directory:   cd infernal-1.1.2

Starting from a source distribution, infernal-1.1.3.tar.gz:

 uncompress:                uncompress infernal-1.1.3.tar.gz  

 unpack:                    tar xf infernal-1.1.3.tar

 move into new directory:   cd infernal-1.1.3

 configure:                 ./configure

 build:                     make

 automated tests:           make check

(IA32, IA64, or Intel64) processor that supports the SSE2 vector

instruction set, or a PowerPC processor that supports the Altivec/VMX

instruction set. If your platform does not support one of these vector

instruction sets, you won’t be able to install and run Infernal 1.1 on

instruction sets, you won't be able to install and run Infernal 1.1 on

it.

-------------------------------------------------------------

Infernal - inference of RNA secondary structural alignments

@INFERNAL_COPYRIGHT@

Copyright (C) 1991-2016      Sean R. Eddy

Copyright (C) 2005-2016      Eric P. Nawrocki

Copyright (C) 1991-2019      Sean R. Eddy

Copyright (C) 2005-2019      Eric P. Nawrocki

Copyright (C) 2005-2011      Diana L. Kolbe

Copyright (C) 2004           Zasha Weinberg

Copyright (C) 1990           Don G.Gilbert

Copyright (C) 2000-2016      Howard Hughes Medical Institute

Copyright (C) 2000-2019      Howard Hughes Medical Institute

Copyright (C) 1995-2006      Washington University School of Medicine

Copyright (C) 1992-1995      MRC Laboratory of Molecular Biology

Copyright (C) 2004           University of Washington, Seattle

VPATH          = @srcdir@

SHELL          = /bin/sh

# location of easel

ESLDIR         = @INFERNAL_ESLDIR@

# location of hmmer

HMMERDIR       = @INFERNAL_HMMERDIR@

# location of suffix array library

SADIR          = @INFERNAL_SADIR@

# impl directory (currently only either 'impl_sse' or '')

CC        = @CC@

CFLAGS    = @CFLAGS@

LDFLAGS   = -static @LDFLAGS@

SIMDFLAGS = @SIMD_CFLAGS@

CPPFLAGS  = @CPPFLAGS@

# Other tools

# We do a 'check' in HMMERDIR/testsuite, not HMMERDIR/ because we

# don't need to run the Easel testsuite twice.

#

# Also, HMMER's 'make check' requires its own easel subdir complete

# with compiled miniapps. This may or may not exist. In working copies

# of the trunk it will exist but won't be compiled (infernal/hmmer/

# will use infernal/easel, not infernal/hmmer/easel). In a released

# version infernal/hmmer/easel won't even exist since we delete it

# prior to creating a release.  So, we take care to have the calling

# of hmmer's testsuite work in either case. If hmmer/easel/ exists we

# copy the required miniapps into it and run 'make check' from

# hmmer/testsuite then delete them. If it doesn't, we create a symlink

# to infernal/easel as infernal/hmmer/easel then we run the testsuite

# and then we delete the symlink. Also, if srcdir/hmmer/easel doesn't

# exist, we symlink it to srcdir/easel because the hmmer testsuite

# needs easel/formats/BLOSUM62 which will only be in srcdir/easel

# (yuck!).

check:

	@command -v python3 >/dev/null 2>&1 || { echo >&2 "python3 is required for 'make check', but is not in your PATH. Aborting."; exit 1; }

	${QUIET_SUBDIR0}${ESLDIR}              ${QUIET_SUBDIR1} tests

	${QUIET_SUBDIR0}${SADIR}               ${QUIET_SUBDIR1} all

	${QUIET_SUBDIR0}${HMMERDIR}            ${QUIET_SUBDIR1} tests

	${QUIET_SUBDIR0}src                    ${QUIET_SUBDIR1} tests

	${QUIET_SUBDIR0}${ESLDIR}              ${QUIET_SUBDIR1} check

	if   test -d ${HMMERDIR}/easel && ! test -e  ${HMMERDIR}/easel/miniapps/esl-afetch;   then cp ${ESLDIR}/miniapps/esl-afetch   ${HMMERDIR}/easel/miniapps; fi

	if   test -d ${HMMERDIR}/easel && ! test -e  ${HMMERDIR}/easel/miniapps/esl-reformat; then cp ${ESLDIR}/miniapps/esl-reformat ${HMMERDIR}/easel/miniapps; fi

	if   test -d ${HMMERDIR}/easel && ! test -e  ${HMMERDIR}/easel/miniapps/esl-sfetch;   then cp ${ESLDIR}/miniapps/esl-sfetch   ${HMMERDIR}/easel/miniapps; fi

	if   test -d ${HMMERDIR}/easel && ! test -e  ${HMMERDIR}/easel/miniapps/esl-sfetch;   then cp ${ESLDIR}/miniapps/esl-shuffle  ${HMMERDIR}/easel/miniapps; fi

	if ! test -d ${HMMERDIR}/easel; then cd ${HMMERDIR}; @LN_S@ ../${ESLDIR} .; cd ..; fi

	if ! test -d ${srcdir}/${HMMERDIR}/easel; then @LN_S@ ${srcdir}/${ESLDIR} ${srcdir}/${HMMERDIR}/easel; fi

	${QUIET_SUBDIR0}${HMMERDIR}/testsuite  ${QUIET_SUBDIR1} check

	if   test -L ${HMMERDIR}/easel; then rm ${HMMERDIR}/easel; fi

	if   test -L ${srcdir}/${HMMERDIR}/easel; then rm ${srcdir}/${HMMERDIR}/easel; fi

	if   test -e ${HMMERDIR}/easel/miniapps/esl-afetch;   then rm ${HMMERDIR}/easel/miniapps/esl-afetch;   fi

	if   test -e ${HMMERDIR}/easel/miniapps/esl-reformat; then rm ${HMMERDIR}/easel/miniapps/esl-reformat; fi

	if   test -e ${HMMERDIR}/easel/miniapps/esl-sfetch;   then rm ${HMMERDIR}/easel/miniapps/esl-sfetch;   fi

	if   test -e ${HMMERDIR}/easel/miniapps/esl-shuffle;  then rm ${HMMERDIR}/easel/miniapps/esl-shuffle;  fi

	${QUIET_SUBDIR0}testsuite              ${QUIET_SUBDIR1} check

# devcheck: Run Infernal developer test suite (slower, but more comprehensive than 'check').

#

devcheck:

	@command -v python3 >/dev/null 2>&1 || { echo >&2 "python3 is required for 'make devcheck', but is not in your PATH. Aborting."; exit 1; }

	${QUIET_SUBDIR0}testsuite  ${QUIET_SUBDIR1} devcheck

# pdf: compile the User Guides.

Infernal - inference of RNA secondary structure alignments

http://eddylab.org/infernal/

Version 1.1.2; July 2016

Copyright (C) 2016 Howard Hughes Medical Institute.

Version 1.1.3; Nov 2019

Copyright (C) 2019 Howard Hughes Medical Institute.

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Infernal is an implementation of covariance models (CMs), which are