Spack view¶
You may have noticed that the final line of our installation output in the previous section ended with
==> Updating view at /data/scratch/abc123/spack-environments/spack-only/.spack-env/view
Let's look at that directory a bit more closely:
Spack view contents
[spack-only] $ ls -1 /data/scratch/${USER}/spack-environments/spack-only/.spack-env/view
bin
conf
docs
etc
include
jmods
legal
lib
lib64
libexec
man
NOTICE
pyvenv.cfg
release
sbin
share
Each directory is vaguely similar to what you might have inside a Conda
environment, a container or an
installation of Linux. There are binaries (bin), config files (etc), shared
libraries (lib/lib64) etc. However, if we look at the disk usage of this
directory, you'll notice that it is very small:
Code output
[spack-only] $ du -hd1 /data/scratch/${USER}/spack-environments/spack-only/.spack-env/view/
3.2M /data/scratch/abc123/spack-environments/spack-only/.spack-env/view/include
1.0K /data/scratch/abc123/spack-environments/spack-only/.spack-env/view/docs
473K /data/scratch/abc123/spack-environments/spack-only/.spack-env/view/man
208K /data/scratch/abc123/spack-environments/spack-only/.spack-env/view/bin
11K /data/scratch/abc123/spack-environments/spack-only/.spack-env/view/conf
1.0K /data/scratch/abc123/spack-environments/spack-only/.spack-env/view/libexec
1.5K /data/scratch/abc123/spack-environments/spack-only/.spack-env/view/etc
43K /data/scratch/abc123/spack-environments/spack-only/.spack-env/view/lib64
36K /data/scratch/abc123/spack-environments/spack-only/.spack-env/view/jmods
5.7M /data/scratch/abc123/spack-environments/spack-only/.spack-env/view/lib
4.7M /data/scratch/abc123/spack-environments/spack-only/.spack-env/view/share
1.6M /data/scratch/abc123/spack-environments/spack-only/.spack-env/view/.spack
156K /data/scratch/abc123/spack-environments/spack-only/.spack-env/view/legal
1.0K /data/scratch/abc123/spack-environments/spack-only/.spack-env/view/sbin
16M /data/scratch/abc123/spack-environments/spack-only/.spack-env/view/
This is because the contents of many directories aren't the actual binaries and
shared libraries, but instead symlinks to them in your install tree: root:
and upstream:
Spack view binary directory (click to expand)
[spack-only] $ ls -lah /data/scratch/${USER}/spack-environments/spack-only/.spack-env/view/bin
total 208K
drwxr-xr-x 2 abc123 qmul 16K May 20 13:23 .
drwxr-xr-x 16 abc123 qmul 4.0K May 20 13:23 ..
lrwxrwxrwx 1 abc123 qmul 94 May 20 13:23 2to3 -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/python/3.11.7-rj3pox3/bin/2to3
lrwxrwxrwx 1 abc123 qmul 99 May 20 13:23 2to3-3.11 -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/python/3.11.7-rj3pox3/bin/2to3-3.11
lrwxrwxrwx 1 abc123 qmul 99 May 20 13:23 ace2sam -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/samtools/1.19.2-z5llbnv/bin/ace2sam
lrwxrwxrwx 1 abc123 qmul 104 May 20 13:23 annotateBed -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bedtools2/2.31.1-pifiw4t/bin/annotateBed
lrwxrwxrwx 1 abc123 qmul 99 May 20 13:23 annot-tsv -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/htslib/1.19.1-x6h2y4a/bin/annot-tsv
lrwxrwxrwx 1 abc123 qmul 100 May 20 13:23 autopoint -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/gettext/0.22.5-udcuonu/bin/autopoint
lrwxrwxrwx 1 abc123 qmul 101 May 20 13:23 bamToBed -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bedtools2/2.31.1-pifiw4t/bin/bamToBed
lrwxrwxrwx 1 abc123 qmul 103 May 20 13:23 bamToFastq -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bedtools2/2.31.1-pifiw4t/bin/bamToFastq
lrwxrwxrwx 1 abc123 qmul 104 May 20 13:23 bed12ToBed6 -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bedtools2/2.31.1-pifiw4t/bin/bed12ToBed6
lrwxrwxrwx 1 abc123 qmul 103 May 20 13:23 bedpeToBam -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bedtools2/2.31.1-pifiw4t/bin/bedpeToBam
lrwxrwxrwx 1 abc123 qmul 101 May 20 13:23 bedToBam -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bedtools2/2.31.1-pifiw4t/bin/bedToBam
lrwxrwxrwx 1 abc123 qmul 101 May 20 13:23 bedToIgv -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bedtools2/2.31.1-pifiw4t/bin/bedToIgv
lrwxrwxrwx 1 abc123 qmul 101 May 20 13:23 bedtools -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bedtools2/2.31.1-pifiw4t/bin/bedtools
lrwxrwxrwx 1 abc123 qmul 95 May 20 13:23 bgzip -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/htslib/1.19.1-x6h2y4a/bin/bgzip
lrwxrwxrwx 1 abc123 qmul 104 May 20 13:23 blast2sam.pl -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/samtools/1.19.2-z5llbnv/bin/blast2sam.pl
lrwxrwxrwx 1 abc123 qmul 111 May 20 13:23 blastdb_aliastool -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/bin/blastdb_aliastool
lrwxrwxrwx 1 abc123 qmul 106 May 20 13:23 blastdbcheck -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/bin/blastdbcheck
lrwxrwxrwx 1 abc123 qmul 104 May 20 13:23 blastdbcmd -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/bin/blastdbcmd
lrwxrwxrwx 1 abc123 qmul 109 May 20 13:23 blastdb_convert -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/bin/blastdb_convert
lrwxrwxrwx 1 abc123 qmul 103 May 20 13:23 blastdbcp -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/bin/blastdbcp
lrwxrwxrwx 1 abc123 qmul 106 May 20 13:23 blastdb_path -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/bin/blastdb_path
lrwxrwxrwx 1 abc123 qmul 109 May 20 13:23 blast_formatter -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/bin/blast_formatter
lrwxrwxrwx 1 abc123 qmul 100 May 20 13:23 blastn -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/bin/blastn
lrwxrwxrwx 1 abc123 qmul 100 May 20 13:23 blastp -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/bin/blastp
lrwxrwxrwx 1 abc123 qmul 106 May 20 13:23 blast_report -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/bin/blast_report
lrwxrwxrwx 1 abc123 qmul 100 May 20 13:23 blastx -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/bin/blastx
lrwxrwxrwx 1 abc123 qmul 97 May 20 13:23 bowtie2 -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bowtie2/2.5.2-a7zexua/bin/bowtie2
lrwxrwxrwx 1 abc123 qmul 105 May 20 13:23 bowtie2-align-l -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bowtie2/2.5.2-a7zexua/bin/bowtie2-align-l
lrwxrwxrwx 1 abc123 qmul 105 May 20 13:23 bowtie2-align-s -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bowtie2/2.5.2-a7zexua/bin/bowtie2-align-s
lrwxrwxrwx 1 abc123 qmul 103 May 20 13:23 bowtie2-build -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bowtie2/2.5.2-a7zexua/bin/bowtie2-build
lrwxrwxrwx 1 abc123 qmul 105 May 20 13:23 bowtie2-build-l -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bowtie2/2.5.2-a7zexua/bin/bowtie2-build-l
lrwxrwxrwx 1 abc123 qmul 105 May 20 13:23 bowtie2-build-s -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bowtie2/2.5.2-a7zexua/bin/bowtie2-build-s
lrwxrwxrwx 1 abc123 qmul 105 May 20 13:23 bowtie2-inspect -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bowtie2/2.5.2-a7zexua/bin/bowtie2-inspect
lrwxrwxrwx 1 abc123 qmul 107 May 20 13:23 bowtie2-inspect-l -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bowtie2/2.5.2-a7zexua/bin/bowtie2-inspect-l
lrwxrwxrwx 1 abc123 qmul 107 May 20 13:23 bowtie2-inspect-s -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bowtie2/2.5.2-a7zexua/bin/bowtie2-inspect-s
lrwxrwxrwx 1 abc123 qmul 105 May 20 13:23 bowtie2sam.pl -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/samtools/1.19.2-z5llbnv/bin/bowtie2sam.pl
lrwxrwxrwx 1 abc123 qmul 95 May 20 13:23 bunzip2 -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/bzip2/1.0.8-uj4wyhx/bin/bunzip2
lrwxrwxrwx 1 abc123 qmul 93 May 20 13:23 bzcat -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/bzip2/1.0.8-uj4wyhx/bin/bzcat
lrwxrwxrwx 1 abc123 qmul 93 May 20 13:23 bzcmp -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/bzip2/1.0.8-uj4wyhx/bin/bzcmp
lrwxrwxrwx 1 abc123 qmul 94 May 20 13:23 bzdiff -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/bzip2/1.0.8-uj4wyhx/bin/bzdiff
lrwxrwxrwx 1 abc123 qmul 95 May 20 13:23 bzegrep -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/bzip2/1.0.8-uj4wyhx/bin/bzegrep
lrwxrwxrwx 1 abc123 qmul 95 May 20 13:23 bzfgrep -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/bzip2/1.0.8-uj4wyhx/bin/bzfgrep
lrwxrwxrwx 1 abc123 qmul 94 May 20 13:23 bzgrep -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/bzip2/1.0.8-uj4wyhx/bin/bzgrep
lrwxrwxrwx 1 abc123 qmul 93 May 20 13:23 bzip2 -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/bzip2/1.0.8-uj4wyhx/bin/bzip2
lrwxrwxrwx 1 abc123 qmul 100 May 20 13:23 bzip2recover -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/bzip2/1.0.8-uj4wyhx/bin/bzip2recover
lrwxrwxrwx 1 abc123 qmul 94 May 20 13:23 bzless -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/bzip2/1.0.8-uj4wyhx/bin/bzless
lrwxrwxrwx 1 abc123 qmul 94 May 20 13:23 bzmore -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/bzip2/1.0.8-uj4wyhx/bin/bzmore
lrwxrwxrwx 1 abc123 qmul 97 May 20 13:23 captoinfo -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/ncurses/6.5-4n2uzha/bin/captoinfo
lrwxrwxrwx 1 abc123 qmul 107 May 20 13:23 cds-mapping-stats -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/spades/3.15.5-ap7kfa4/bin/cds-mapping-stats
lrwxrwxrwx 1 abc123 qmul 103 May 20 13:23 cds-subgraphs -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/spades/3.15.5-ap7kfa4/bin/cds-subgraphs
lrwxrwxrwx 1 abc123 qmul 97 May 20 13:23 certtool -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/gnutls/3.8.3-fwxsw34/bin/certtool
lrwxrwxrwx 1 abc123 qmul 101 May 20 13:23 cjpeg -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/libjpeg-turbo/3.0.0-wclh6t6/bin/cjpeg
lrwxrwxrwx 1 abc123 qmul 120 May 20 13:23 cleanup-blastdb-volumes.py -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/bin/cleanup-blastdb-volumes.py
lrwxrwxrwx 1 abc123 qmul 93 May 20 13:23 clear -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/ncurses/6.5-4n2uzha/bin/clear
lrwxrwxrwx 1 abc123 qmul 103 May 20 13:23 closestBed -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bedtools2/2.31.1-pifiw4t/bin/closestBed
lrwxrwxrwx 1 abc123 qmul 103 May 20 13:23 clusterBed -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bedtools2/2.31.1-pifiw4t/bin/clusterBed
lrwxrwxrwx 1 abc123 qmul 106 May 20 13:23 complementBed -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bedtools2/2.31.1-pifiw4t/bin/complementBed
lrwxrwxrwx 1 abc123 qmul 111 May 20 13:23 convert2blastmask -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/bin/convert2blastmask
lrwxrwxrwx 1 abc123 qmul 96 May 20 13:23 corelist -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/perl/5.38.0-eyk53wh/bin/corelist
lrwxrwxrwx 1 abc123 qmul 105 May 20 13:23 coronaspades.py -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/spades/3.15.5-ap7kfa4/bin/coronaspades.py
lrwxrwxrwx 1 abc123 qmul 104 May 20 13:23 coverageBed -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bedtools2/2.31.1-pifiw4t/bin/coverageBed
lrwxrwxrwx 1 abc123 qmul 92 May 20 13:23 cpan -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/perl/5.38.0-eyk53wh/bin/cpan
lrwxrwxrwx 1 abc123 qmul 93 May 20 13:23 cpanm -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/perl/5.38.0-eyk53wh/bin/cpanm
lrwxrwxrwx 1 abc123 qmul 98 May 20 13:23 c_rehash -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/openssl/3.3.0-filwsx6/bin/c_rehash
lrwxrwxrwx 1 abc123 qmul 91 May 20 13:23 curl -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/curl/8.7.1-v4za2y6/bin/curl
lrwxrwxrwx 1 abc123 qmul 98 May 20 13:23 curl-config -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/curl/8.7.1-v4za2y6/bin/curl-config
(etc.)
Spack view shared library directory (click to expand)
[spack-only] $ ls -lah /data/scratch/${USER}/spack-environments/spack-only/.spack-env/view/lib
total 283K
drwxr-xr-x 12 abc123 qmul 32K May 20 13:23 .
drwxr-xr-x 16 abc123 qmul 4.0K May 20 13:23 ..
drwxr-xr-x 54 abc123 qmul 8.0K May 20 13:23 5.38.0
lrwxrwxrwx 1 abc123 qmul 104 May 20 13:23 classlist -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/openjdk/17.0.8.1_1-qk5wpoh/lib/classlist
drwxr-xr-x 4 abc123 qmul 4.0K May 20 13:23 cmake
lrwxrwxrwx 1 abc123 qmul 101 May 20 13:23 ct.sym -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/openjdk/17.0.8.1_1-qk5wpoh/lib/ct.sym
drwxr-xr-x 2 abc123 qmul 4.0K May 20 13:23 gettext
lrwxrwxrwx 1 abc123 qmul 100 May 20 13:23 jexec -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/openjdk/17.0.8.1_1-qk5wpoh/lib/jexec
drwxr-xr-x 2 abc123 qmul 4.0K May 20 13:23 jfr
lrwxrwxrwx 1 abc123 qmul 105 May 20 13:23 jrt-fs.jar -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/openjdk/17.0.8.1_1-qk5wpoh/lib/jrt-fs.jar
lrwxrwxrwx 1 abc123 qmul 107 May 20 13:23 jspawnhelper -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/openjdk/17.0.8.1_1-qk5wpoh/lib/jspawnhelper
lrwxrwxrwx 1 abc123 qmul 102 May 20 13:23 jvm.cfg -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/openjdk/17.0.8.1_1-qk5wpoh/lib/jvm.cfg
lrwxrwxrwx 1 abc123 qmul 106 May 20 13:23 libaccess.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/lib/libaccess.so
lrwxrwxrwx 1 abc123 qmul 112 May 20 13:23 libalign_format.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/lib/libalign_format.so
lrwxrwxrwx 1 abc123 qmul 107 May 20 13:23 libasan.so.8 -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/gcc-runtime/12.2.0-w77gg5r/lib/libasan.so.8
lrwxrwxrwx 1 abc123 qmul 104 May 20 13:23 libasprintf.a -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/gettext/0.22.5-udcuonu/lib/libasprintf.a
lrwxrwxrwx 1 abc123 qmul 105 May 20 13:23 libasprintf.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/gettext/0.22.5-udcuonu/lib/libasprintf.so
lrwxrwxrwx 1 abc123 qmul 107 May 20 13:23 libasprintf.so.0 -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/gettext/0.22.5-udcuonu/lib/libasprintf.so.0
lrwxrwxrwx 1 abc123 qmul 111 May 20 13:23 libasprintf.so.0.0.0 -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/gettext/0.22.5-udcuonu/lib/libasprintf.so.0.0.0
lrwxrwxrwx 1 abc123 qmul 109 May 20 13:23 libatomic.so.1 -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/gcc-runtime/12.2.0-w77gg5r/lib/libatomic.so.1
lrwxrwxrwx 1 abc123 qmul 107 May 20 13:23 libattach.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/openjdk/17.0.8.1_1-qk5wpoh/lib/libattach.so
lrwxrwxrwx 1 abc123 qmul 113 May 20 13:23 libawt_headless.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/openjdk/17.0.8.1_1-qk5wpoh/lib/libawt_headless.so
lrwxrwxrwx 1 abc123 qmul 104 May 20 13:23 libawt.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/openjdk/17.0.8.1_1-qk5wpoh/lib/libawt.so
lrwxrwxrwx 1 abc123 qmul 109 May 20 13:23 libawt_xawt.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/openjdk/17.0.8.1_1-qk5wpoh/lib/libawt_xawt.so
lrwxrwxrwx 1 abc123 qmul 106 May 20 13:23 libbiblio.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/lib/libbiblio.so
lrwxrwxrwx 1 abc123 qmul 107 May 20 13:23 libbiotree.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/lib/libbiotree.so
lrwxrwxrwx 1 abc123 qmul 113 May 20 13:23 libblast_app_util.a -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/lib/libblast_app_util.a
lrwxrwxrwx 1 abc123 qmul 120 May 20 13:23 libblast_app_util-static.a -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/lib/libblast_app_util-static.a
lrwxrwxrwx 1 abc123 qmul 114 May 20 13:23 libblastdb_format.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/lib/libblastdb_format.so
lrwxrwxrwx 1 abc123 qmul 107 May 20 13:23 libblastdb.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/lib/libblastdb.so
lrwxrwxrwx 1 abc123 qmul 110 May 20 13:23 libblastinput.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/lib/libblastinput.so
lrwxrwxrwx 1 abc123 qmul 114 May 20 13:23 libblast_services.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/lib/libblast_services.so
lrwxrwxrwx 1 abc123 qmul 105 May 20 13:23 libblast.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/lib/libblast.so
lrwxrwxrwx 1 abc123 qmul 109 May 20 13:23 libblastxml2.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/lib/libblastxml2.so
lrwxrwxrwx 1 abc123 qmul 108 May 20 13:23 libblastxml.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/lib/libblastxml.so
lrwxrwxrwx 1 abc123 qmul 98 May 20 13:23 libbsd.a -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/libbsd/0.12.1-zb23l3j/lib/libbsd.a
lrwxrwxrwx 1 abc123 qmul 103 May 20 13:23 libbsd-ctor.a -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/libbsd/0.12.1-zb23l3j/lib/libbsd-ctor.a
lrwxrwxrwx 1 abc123 qmul 99 May 20 13:23 libbsd.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/libbsd/0.12.1-zb23l3j/lib/libbsd.so
lrwxrwxrwx 1 abc123 qmul 101 May 20 13:23 libbsd.so.0 -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/libbsd/0.12.1-zb23l3j/lib/libbsd.so.0
lrwxrwxrwx 1 abc123 qmul 106 May 20 13:23 libbsd.so.0.12.1 -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/libbsd/0.12.1-zb23l3j/lib/libbsd.so.0.12.1
lrwxrwxrwx 1 abc123 qmul 96 May 20 13:23 libbz2.a -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/bzip2/1.0.8-uj4wyhx/lib/libbz2.a
lrwxrwxrwx 1 abc123 qmul 97 May 20 13:23 libbz2.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/bzip2/1.0.8-uj4wyhx/lib/libbz2.so
lrwxrwxrwx 1 abc123 qmul 99 May 20 13:23 libbz2.so.1 -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/bzip2/1.0.8-uj4wyhx/lib/libbz2.so.1
lrwxrwxrwx 1 abc123 qmul 101 May 20 13:23 libbz2.so.1.0 -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/bzip2/1.0.8-uj4wyhx/lib/libbz2.so.1.0
lrwxrwxrwx 1 abc123 qmul 103 May 20 13:23 libbz2.so.1.0.8 -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/bzip2/1.0.8-uj4wyhx/lib/libbz2.so.1.0.8
lrwxrwxrwx 1 abc123 qmul 103 May 20 13:23 libcdd.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/lib/libcdd.so
lrwxrwxrwx 1 abc123 qmul 104 May 20 13:23 libcn3d.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/lib/libcn3d.so
lrwxrwxrwx 1 abc123 qmul 122 May 20 13:23 libcomposition_adjustment.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/lib/libcomposition_adjustment.so
lrwxrwxrwx 1 abc123 qmul 107 May 20 13:23 libconnect.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/lib/libconnect.so
lrwxrwxrwx 1 abc123 qmul 107 May 20 13:23 libconnext.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/lib/libconnext.so
lrwxrwxrwx 1 abc123 qmul 107 May 20 13:23 libconnssl.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do/lib/libconnssl.so
lrwxrwxrwx 1 abc123 qmul 103 May 20 13:23 libcrypt.a -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/libxcrypt/4.4.35-4mszlpj/lib/libcrypt.a
lrwxrwxrwx 1 abc123 qmul 104 May 20 13:23 libcrypt.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/libxcrypt/4.4.35-4mszlpj/lib/libcrypt.so
lrwxrwxrwx 1 abc123 qmul 106 May 20 13:23 libcrypt.so.2 -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/libxcrypt/4.4.35-4mszlpj/lib/libcrypt.so.2
lrwxrwxrwx 1 abc123 qmul 110 May 20 13:23 libcrypt.so.2.0.0 -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/libxcrypt/4.4.35-4mszlpj/lib/libcrypt.so.2.0.0
lrwxrwxrwx 1 abc123 qmul 96 May 20 13:23 libcurl.a -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/curl/8.7.1-v4za2y6/lib/libcurl.a
lrwxrwxrwx 1 abc123 qmul 97 May 20 13:23 libcurl.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/curl/8.7.1-v4za2y6/lib/libcurl.so
lrwxrwxrwx 1 abc123 qmul 99 May 20 13:23 libcurl.so.4 -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/curl/8.7.1-v4za2y6/lib/libcurl.so.4
lrwxrwxrwx 1 abc123 qmul 103 May 20 13:23 libcurl.so.4.8.0 -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/curl/8.7.1-v4za2y6/lib/libcurl.so.4.8.0
lrwxrwxrwx 1 abc123 qmul 100 May 20 13:23 libcurses.so -> /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/ncurses/6.5-4n2uzha/lib/libcurses.so
(etc.)
You'll also find that the binaries for the applications you listed in the
specs section of your spack.yaml file are all simultaneously available in
your activated environment:
Spack environment applications (click to expand)
[spack-only] $ bedtools --version
bedtools v2.31.1
[spack-only] $ blastp -version
blastp: 2.14.1+
Package: blast 2.14.1, build Jun 6 2024 17:37:20
[spack-only] $ bowtie2 --version
/share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bowtie2/2.5.2-a7zexua/bin/bowtie2-align-s version 2.5.2
64-bit
Built on ddy57
Mon Mar 10 15:01:31 UTC 2025
Compiler: gcc version 12.2.0 (Spack GCC)
Options: -O3 -msse2 -funroll-loops -g3 -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
[spack-only] $ gatk -version
Using GATK jar /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/gatk/4.5.0.0-6uwwf26/bin/gatk-package-4.5.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/gatk/4.5.0.0-6uwwf26/bin/gatk-package-4.5.0.0-local.jar -version
The Genome Analysis Toolkit (GATK) v4.5.0.0
HTSJDK Version: 4.1.0
Picard Version: 3.1.1
[spack-only] $ qctool_v2.2.0 -help
Welcome to qctool
(version: 2.2.0, revision: unknown)
(C) 2009-2020 University of Oxford
Usage: qctool <options>
OPTIONS:
(etc.)
[spack-only] $ samtools --version
samtools 1.19.2
Using htslib 1.19.1
Copyright (C) 2024 Genome Research Ltd.
(etc.)
[spack-only] $ spades.py --version
SPAdes genome assembler v3.15.5