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## installing_singularity_on_macbook_pro_m1_pro.md

      
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              July 29, 2023 19:25
            
              
                This Gist describes the steps needed to install Singularity in a Parallels-Desktop-and-vagrant-managed arm64-compatible virtual machine on a MacBook Pro with an M1 Pro chip.
              
          
    I wanted to install Singularity on my M1 Pro (Ventura 13.1).
As this chip is arm64 based, it turned out rather tricky.
Some resources that I consulted although none of them presented a self-contained solution are below.
I hadn't tried the solution via UTM as I had access to a Parallels Desktop license and did not necessarily want to have yet-another-tool installed.

Instructions from Singularity itself: https://docs.sylabs.io/guides/3.0/user-guide/installation.html#install-on-windows-or-mac
Video using UTM:
https://www.youtube.com/watch?v=aKHbaytlS00
https://github.com/manuparra/singularitycontainers-on-m1-arm64
Another set of general instructions.: https://github.com/sPHENIX-Collaboration/Singularity/blob/master/OSX_installationguide.md


## gist:4a1e25ae465039a5d76c11018afe4466
http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&RID=REPLACE-BY-YOUR-RID&FORMAT_TYPE=CSV&FORMAT_OBJECT=Alignment&ALIGNMENT_VIEW=Tabular&CMD=Get

## gist:8ed853e209d64941907195fea8aa289e
doneCompiling sdm..
make: Entering directory '/home/cedric/apps/software/lotus_pipeline_1.57/sdm_src'
g++  -O3 -std=c++0x  -D__USE_XOPEN2K8   -c -o Demultipl.o Demultipl.cpp
g++  -O3 -std=c++0x  -D__USE_XOPEN2K8   -c -o containers.o containers.cpp
g++  -O3 -std=c++0x  -D__USE_XOPEN2K8   -c -o IO.o IO.cpp
g++  -O3 -std=c++0x  -D__USE_XOPEN2K8   -c -o InputStream.o InputStream.cpp
g++  -O3 -std=c++0x  -D__USE_XOPEN2K8   -c -o DNAconsts.o DNAconsts.cpp
g++  -O3 -std=c++0x  -D__USE_XOPEN2K8      Demultipl.o containers.o IO.o InputStream.o DNAconsts.o -lz -o sdm
make: Leaving directory '/home/cedric/apps/software/lotus_pipeline_1.57/sdm_src'
Installing sdm:

## adonis_output.txt
Call:
adonis(formula = GPfr_phylum_bray ~ SampleType, data = sampledf)

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model     R2 Pr(>F)
SampleType  8    8.2618 1.03272    5.81 0.7322  0.001 ***

## skeleton.mk
SHELL = /bin/bash

DDIR = data
RDIR = results
SDIR = src

SAMPLES = S1 S2 S3
DOUBLED_SAMPLES = $(foreach sample, $(SAMPLES), $(sample)/$(sample))

####################

## gist:3366f6b29680e0c357d2068e09b09f6e
grep -E "^[0-9]*-" -A1 compare.abundtrim.dist.txt | tr -d "\n" | sed 's/]/]\n/g' | tr -s " " "\t" | sed 's/\[\t//' | sed 's/\]//'

## Makefile.amplicon_minion.benitez-paez_sanz
SHELL = /bin/bash

DDIR = orig_data
RDIR = results

PORETOOLS_BIN = . venv/bin/activate; poretools
PULLSEQ_BIN = ml vizbins_little_helpers; pullseq

MIN_LENGTH ?= 1000

## fuzzymatch_titles.py
from fuzzywuzzy import fuzz
from fuzzywuzzy import process
from collections import Counter

A_title_file = "/tmp/A_titles.txt"
B_title_file = "/tmp/B_titles.txt"

# Open the files and get the titles
A_titles = []
with open(A_title_file) as f:

## fit_and_plot_normal_mixtures.R
library(ggplot2)
library(plyr)
library(mixtools)

###
# GLOBAL THEME AND GLOBAL AESTHETICS
###
old <- theme_set(theme_bw() +
                   theme(text = element_text(size=12),
                         axis.title = element_text(size = 14, face="bold"),

## compute_coverage.mk
SHELL=/bin/bash

SAMPLE?=<YOUR_SAMPLE>
DOUBLED_SAMPLE = $(SAMPLE)/$(SAMPLE)

RDIR?=results
DDIR?=data

#####
# BEAUTY TARGETS
	doneCompiling sdm..
	make: Entering directory '/home/cedric/apps/software/lotus_pipeline_1.57/sdm_src'
	g++ -O3 -std=c++0x -D__USE_XOPEN2K8 -c -o Demultipl.o Demultipl.cpp
	g++ -O3 -std=c++0x -D__USE_XOPEN2K8 -c -o containers.o containers.cpp
	g++ -O3 -std=c++0x -D__USE_XOPEN2K8 -c -o IO.o IO.cpp
	g++ -O3 -std=c++0x -D__USE_XOPEN2K8 -c -o InputStream.o InputStream.cpp
	g++ -O3 -std=c++0x -D__USE_XOPEN2K8 -c -o DNAconsts.o DNAconsts.cpp
	g++ -O3 -std=c++0x -D__USE_XOPEN2K8 Demultipl.o containers.o IO.o InputStream.o DNAconsts.o -lz -o sdm
	make: Leaving directory '/home/cedric/apps/software/lotus_pipeline_1.57/sdm_src'
	Installing sdm:
	Call:
	adonis(formula = GPfr_phylum_bray ~ SampleType, data = sampledf)

	Permutation: free
	Number of permutations: 999

	Terms added sequentially (first to last)

	Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
	SampleType 8 8.2618 1.03272 5.81 0.7322 0.001 ***
	SHELL = /bin/bash

	DDIR = data
	RDIR = results
	SDIR = src

	SAMPLES = S1 S2 S3
	DOUBLED_SAMPLES = $(foreach sample, $(SAMPLES), $(sample)/$(sample))

	####################
	SHELL = /bin/bash

	DDIR = orig_data
	RDIR = results

	PORETOOLS_BIN = . venv/bin/activate; poretools
	PULLSEQ_BIN = ml vizbins_little_helpers; pullseq

	MIN_LENGTH ?= 1000
	from fuzzywuzzy import fuzz
	from fuzzywuzzy import process
	from collections import Counter

	A_title_file = "/tmp/A_titles.txt"
	B_title_file = "/tmp/B_titles.txt"

	# Open the files and get the titles
	A_titles = []
	with open(A_title_file) as f:
	library(ggplot2)
	library(plyr)
	library(mixtools)

	###
	# GLOBAL THEME AND GLOBAL AESTHETICS
	###
	old <- theme_set(theme_bw() +
	theme(text = element_text(size=12),
	axis.title = element_text(size = 14, face="bold"),
	SHELL=/bin/bash

	SAMPLE?=<YOUR_SAMPLE>
	DOUBLED_SAMPLE = $(SAMPLE)/$(SAMPLE)

	RDIR?=results
	DDIR?=data

	#####
	# BEAUTY TARGETS