I have some FORS2 spectroscopic data and need to get tools to reduce it.
From the FORS2 page, https://www.eso.org/sci/facilities/paranal/instruments/fors/overview.html, I navigate to the “Manuals”, https://www.eso.org/sci/facilities/paranal/instruments/fors/doc.html.
There, I was redirected to the pipeline recipes to reduce FORS data, https://www.eso.org/sci/software/pipelines/fors/fors-pipe-recipes.html
There, after reading the version introduction, I proceeded to the installation section of the version 5.5.6 for FORS pipeline recipes.
My mac runs the OSX El Capitan, 10.11.6, so it meets the system requirements.
Installation needs to be done with MacPorts package, https://www.eso.org/sci/software/pipelines/installation/macports.html
I check the prerequisites.
1. Macports
I used the instructions on the following website,
https://guide.macports.org/
iMacStone:~ mariastone$ port -version
-bash: port: command not found
So I need to install macports. But, hei, for that I need to install XCode and Xcode command line tools!
https://www.macports.org/install.php
https://developer.apple.com/download/more/ -> I needed my Apple ID and password!
downloaded Xcode_12.4.xip , but found out that it was not good for me ,because I have an older operating system, so I downloaded Xcode 8.2.1, the last version supporting OSX 10.11.5 El Capitan.
https://stackoverflow.com/questions/10335747/how-to-download-xcode-dmg-or-xip-file
It takes a while to download this file …. from Apple Developers website
double click on the .xip file
I get an error
The operation couldn’t be completed . Block-compressed payload operation failed…
trying with the Terminal
https://osxdaily.com/2018/11/02/open-extract-xip-file-mac/
iMacStone:Downloads mariastone$ xip -x Xcode_8.2.1.xip
xip: signing certificate was “Software Update” (validation not attempted)
I had to delete some files and apps to make space on my computer.
Then Xcode seemed to have been installed
Now to download macports, back to https://www.macports.org/install.php
iMacStone:~ mariastone$ sudo xcodebuild -license
I am very busy, and this is taking too long. …..
https://www.macports.org/install.php#installing
downloaded the file MacPorts-2.6.4-10.11-ElCapitan.pkg
double-clicked, and followed the prompts (mostly clicking OK)
2. Xcode
I used the instructions on the following website, to be precise, the answer by “Siavash Alp”
https://stackoverflow.com/questions/21272479/how-can-i-find-out-if-i-have-xcode-commandline-tools-installed
Then I followed the commands per the instructions, https://www.eso.org/sci/software/pipelines/installation/macports.html
iMacStone:~ mariastone$ curl ftp://ftp.eso.org/pub/dfs/pipelines/repositories/stable/macports/setup/Portfile -o Portfile
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 6304 100 6304 0 0 3748 0 0:00:01 0:00:01 –:–:– 3747
iMacStone:~ mariastone$ sudo port sync
Password:
sudo: port: command not found
hmm… what’s going on?
iMacStone:~ mariastone$ port -version
-bash: port: command not found
Did I not install the MacPorts?
iMacStone:~ mariastone$ xcode-select -version
xcode-select version 2343.
iMacStone:~ mariastone$ xcodebuild -version
Xcode 8.2.1
Build version 8C1002
iMacStone:~ mariastone$ gcc –version
Configured with: –prefix=/Applications/Xcode.app/Contents/Developer/usr –with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 8.0.0 (clang-800.0.42.1)
Target: x86_64-apple-darwin15.6.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
installing macports needs XQuartz
downloaded the XQuartz-2.7.11.dmg
double clicked on the .dmg file
double clicked on the XQuartz icon
I have to log out and log back in to make the XQuartz my default X11 tool.
iMacStone:~ mariastone$ sudo port sync
Password:
—> Updating the ports tree
iMacStone:~ mariastone$ port -version
Usage: port
[-bcdfknNopqRstuvy] [-D portdir|portname] [-F cmdfile] action [actionflags]
[[portname|pseudo-portname|port-url] [@version] [+-variant]… [option=value]…]…
“port help” or “man 1 port” for more information.
oopsies, I forgot a command “sudo port install”
iMacStone:~ mariastone$ sudo port install
—> Fetching distfiles for esorepo
—> Verifying checksums for esorepo
—> Extracting esorepo
—> Configuring esorepo
—> Building esorepo
—> Staging esorepo into destroot
—> Installing esorepo @1.3_0
—> Activating esorepo @1.3_0
—> Cleaning esorepo
—> Some of the ports you installed have notes:
esorepo has the following notes:
*** Please run ‘sudo port sync’ to synchronise with the ESO repository. ***
iMacStone:~ mariastone$ sudo port sync
—> Updating the ports tree
to install the pipelines, I continue following the commands on the website
iMacStone:~ mariastone$ port list ‘esopipe-*-all’
esopipe-amber-all @4.4.0 science/esopipe-amber-all
esopipe-crire-all @2.3.11 science/esopipe-crire-all
esopipe-detmon-all @1.3.6 science/esopipe-detmon-all
esopipe-efosc-all @2.3.6 science/esopipe-efosc-all
esopipe-esotk-all @0.9.1 science/esopipe-esotk-all
esopipe-espda-all @1.2.0 science/esopipe-espda-all
esopipe-espdr-all @2.2.1 science/esopipe-espdr-all
esopipe-fors-all @5.5.6 science/esopipe-fors-all
esopipe-giraf-all @2.16.7 science/esopipe-giraf-all
esopipe-gravity-all @1.4.1 science/esopipe-gravity-all
esopipe-hawki-all @2.4.8 science/esopipe-hawki-all
esopipe-iiinstrument-all @0.1.12 science/esopipe-iiinstrument-all
esopipe-isaac-all @6.1.9 science/esopipe-isaac-all
esopipe-kmos-all @3.0.1 science/esopipe-kmos-all
esopipe-matisse-all @1.5.1 science/esopipe-matisse-all
esopipe-midi-all @2.9.1 science/esopipe-midi-all
esopipe-molecfit-all @3.0.3 science/esopipe-molecfit-all
esopipe-muse-all @2.8.4 science/esopipe-muse-all
esopipe-naco-all @4.4.9 science/esopipe-naco-all
esopipe-sinfo-all @3.3.0 science/esopipe-sinfo-all
esopipe-sofi-all @1.5.12 science/esopipe-sofi-all
esopipe-spher-all @0.40.0 science/esopipe-spher-all
esopipe-uves-all @6.1.3 science/esopipe-uves-all
esopipe-vcam-all @2.3.6 science/esopipe-vcam-all
esopipe-vimos-all @4.1.1 science/esopipe-vimos-all
esopipe-visir-all @4.3.10 science/esopipe-visir-all
esopipe-xshoo-all @3.5.0 science/esopipe-xshoo-all
iMacStone:~ mariastone$ sudo port install esopipe-fors-all
—> Computing dependencies for esopipe-fors-all
The following dependencies will be installed:
OpenBLAS
Xft2
brotli
bzip2
cairo
cext
cfitsio
cpl
cython_select
db48
erfa
esopipe-fors
esopipe-fors-datademo
esopipe-fors-datastatic
esopipe-fors-gui
esopipe-fors-recipes
esopipe-fors-wkf
esoreflex
esorex
expat
fftw-3
fftw-3-single
font-adobe-100dpi
font-adobe-75dpi
font-adobe-utopia-100dpi
font-adobe-utopia-75dpi
font-adobe-utopia-type1
font-alias
font-arabic-misc
font-bh-100dpi
font-bh-75dpi
font-bh-lucidatypewriter-100dpi
font-bh-lucidatypewriter-75dpi
font-bh-ttf
font-bh-type1
font-bitstream-100dpi
font-bitstream-75dpi
font-bitstream-speedo
font-bitstream-type1
font-cronyx-cyrillic
font-cursor-misc
font-daewoo-misc
font-dec-misc
font-ibm-type1
font-isas-misc
font-jis-misc
font-micro-misc
font-misc-cyrillic
font-misc-ethiopic
font-misc-meltho
font-misc-misc
font-mutt-misc
font-schumacher-misc
font-screen-cyrillic
font-sony-misc
font-sun-misc
font-winitzki-cyrillic
font-xfree86-type1
fontconfig
freetype
gdbm
gettext
giflib
glib2
gsl
icu
jbigkit
lcms2
legacy-support
libedit
libffi
libgcc
libgcc10
libiconv
libjpeg-turbo
libpixman
libpng
libxml2
luit
lz4
mkfontscale
ncurses
nosetests_select
openjdk11
openjpeg
openssl
ossp-uuid
pcre
perl5.28
pip_select
py36-Pillow
py36-astropy
py36-cairo
py36-cycler
py36-cython
py36-dateutil
py36-kiwisolver
py36-matplotlib
py36-nose
py36-numpy
py36-olefile
py36-parsing
py36-pathlib2
py36-pip
py36-pyerfa
py36-pyobjc
py36-setuptools
py36-sip
py36-six
py36-tkinter
py36-tornado
py36-tz
py36-wxpython-4.0
python36
python3_select
python_select
qhull
quartz-wm
readline
sqlite3
tcl
tiff
tk
wcslib
webp
wxWidgets-3.2
wxWidgets-common
wxWidgets_select
xauth
xinit
xkbcomp
xkeyboard-config
xorg-encodings
xorg-fonts
xorg-libAppleWM
xorg-libX11
xorg-libXScrnSaver
xorg-libXau
xorg-libXaw
xorg-libXdmcp
xorg-libXext
xorg-libXfixes
xorg-libXfont
xorg-libXfont2
xorg-libXfontcache
xorg-libXinerama
xorg-libXmu
xorg-libXp
xorg-libXrandr
xorg-libXt
xorg-libfontenc
xorg-libice
xorg-libpthread-stubs
xorg-libsm
xorg-libxcb
xorg-libxkbfile
xorg-server
xorg-xcb-proto
xorg-xcb-util
xorg-xorgproto
xpm
xrdb
xrender
xset
xterm
xz
zlib
zstd
Continue? [Y/n]:
I clicked “Y” and pressed “ENTER”.
Continue? [Y/n]: Y
—> Fetching archive for esopipe-fors-datastatic
—> Attempting to fetch esopipe-fors-datastatic-5.5.6_0.darwin_15.noarch.tbz2 from ftp://ftp.eso.org/pub/dfs/pipelines/repositories/stable/macports/packages/esopipe-fors-datastatic
—> Attempting to fetch esopipe-fors-datastatic-5.5.6_0.darwin_15.noarch.tbz2.rmd160 from ftp://ftp.eso.org/pub/dfs/pipelines/repositories/stable/macports/packages/esopipe-fors-datastatic
—> Installing esopipe-fors-datastatic @5.5.6_0
—> Activating esopipe-fors-datastatic @5.5.6_0
—> Cleaning esopipe-fors-datastatic
—> Fetching archive for zlib
….
for the rest, I also answered “Y” and clicked ENTER.
iMacStone:~ mariastone$ esoreflex
The base dir is /opt/local/share/esoreflex-2.11.0
Kepler.run going to run.setMain(org.kepler.Kepler)
JVM Memory: min = 256m, max = 4096m, stack = 1m
setting dock icon to -Xdock:icon=/opt/local/share/esoreflex-2.11.0/common/resources/icons/kepler-dock-icon.png
Set environment variable: PATH
….
Kepler window openned up
#in a different iTerm window
iMacStone:~ mariastone$ esorex recipe data.sof
***** ESO Recipe Execution Tool, version 3.13.3 *****
[ ERROR ] esorex: Unable to find recipe ‘recipe’. Check that the recipe is in the path specified by the ‘–recipe-dir’ option.
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