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A list of currently available modules globally available (after a bit of massaging) is presented below for your convenience. The listing is generated with module -t spider; feel free to run this yourself if you'd prefer to navigate with grep instead of CTRL/CMD+F (you'll need to use --redirect if you want to parse in the terminal; see the below block title for the exact command used).

For more information about a specific module, type module spider SPECIFICMODULE (substituted from the list) to get more output.

As a reminder, if you'd like to search for software by type, module keyword is available (for example, try typing module keyword seq and see what shows up). We try to make the keywords for modules appropriate, but when in doubt, consult the full list.

If there is an application and/or version that you would like but don't see on this list, feel free to submit a ticket with us (either via the website or by emailing rchelp@hms.harvard.edu). Keep in mind that you can also install software yourself under most circumstances, so if you'd prefer not to wait for us to get back to you, you can give it a try yourself. We provide generic instructions and suggestions at Local Software Installs, and we can assist you as well.

This list is generated by running `module -t --redirect spider | grep -v /$`

Modules list as of Oct 25 2020

SoftwareVersion(s)
aligntk1.0.2
alnpack2.1
annovar20160201-patched , 20170601
ashlar1.11.1 , 1.12.0 , 1.7.0
atlas3.10.3
bamreadcount0.8.0
bamtools2.4.1
bcbiolatest
bcftools1.10.2 , 1.3.1 , 1.9
bcl2fastq2.17.1.14 , 2.18.0.12 , 2.19.1.403 , 2.20.0.422
bedops2.4.30
bedtools2.26.0 , 2.27.1
beta1.0.7
bioformats2ometiff0.1 , 0.2.1 , 0.2.2 , 0.2.6
biogridslatest
bio-samtools1.43
bison3.0.4
blast2.10.1+ , 2.6.0+
blast-legacy2.2.26
blat35
boost1.57.0 , 1.57.0.gcc.4.8.5 , 1.62.0
bowtie1.2.1.1 , 1.2.2
bowtie22.2.9 , 2.3.4.3
breseq0.29.0 , 0.32.0
bwa0.6.2 , 0.7.15 , 0.7.17 , 0.7.8
caffe1.0
cairo1.14.6 , 1.14.6-R
cdhit4.6.8
cellranger2.1.1 , 2.2.0 , 3.0.0 , 3.0.2 , 3.1.0 , 4.0.0
cellranger-ATAC1.0.1 , 1.1.0
cmake3.14.1 , 3.7.1 , 3.7.1.gcc.4.8.5
CNVnator0.3.3
conda24.2.13
csubmitterlatest
cuda10.0 , 10.1 , 10.2 , 8.0 , 9.0
cufflinks2.2.1
cutadapt1.14 , 2.5
cython0.25.1
datamash1.2
deeptools2.5.3 , 3.0.0 , 3.0.2
fastqc0.10.1 , 0.11.3 , 0.11.5
fastq_screen0.11.2
fastx0.0.13
ffmpeg3.3.3
fftw3.3.6-pl1 , 3.3.6-pl1-mpi , 3.3.6-pl1_mpi_gcc-4.8.5 , 3.3.7
fiji2 , 2.11292018
fontconfig2.12.1
freebayes1.3.2
freetds1.00.84
freetype2.7
gatk3.5 , 3.7 , 4.0.0.0
gcc4.7.4 , 4.8.5 , 6.2.0 , 9.2.0
gdal3.0.2
gdb7.12
gdc-client1.3.0
gemini0.30.2
genrich0.6
geos3.8.1
ghostscript9.21 , 9.24
git2.9.5
glib2.50.2 , 2.56.1
gmap-gsnap2018.02.12
gnuplot5.0.5
go1.13 , 1.9.2
gobject1.54.1
graph-tool2.26
graphviz2.40.1
gromacs2018.2 , 2018.2.gpu , 2020.1 , 2020.1.gpu
gsl2.3 , 2.6
gurobi8.1.1
harfbuzz1.3.4
hdf51.10.1 , 1.10.1-gcc-4.8.5 , 1.12.0
hisat22.0.5 , 2.1.0
hmmer3.2.1
homer4.10.3 , 4.9
htseq0.12.4 , 0.9.1
htslib1.10.2 , 1.3.2 , 1.9.0
ice3.5.1 , 3.6.4
idr2.0.2
igv2.3.97 , 2.4.9
igvtools2.3.88 , 2.3.98
imageJ1.51r
imageMagick6.9.1.10
intel2016
itasser5.1
javajdk-1.7u80 , jdk-1.8u112
jellyfish2.2.6
jpeg9b
kallisto0.43.1 , 0.45.1
lapacke3.6.1
libffi3.2.1
libpng1.2.59 , 1.6.26
libxml2.9.4
lmod7.5.17
macs22.1.1.20160309
mageck0.5.6 , 0.5.9.4
mathematica11.2.0 , 12.1.1
matlab2016b , 2017a , 2017b , 2018a , 2018b , 2019a , 2019b , 2020a
meme4.12.0 , 4.12.0-serial , 5.0.2 , 5.0.3
multiqc1.3 , 1.5 , 1.9
mysql55
namd2020
novoalign3.09.01
nupack3.2.2
omero5.2.5.42 , 5.4.10.46 , 5.4.10.56 , 5.4.10.65 , 5.4.5.18 , 5.4.6.21 , 5.4.7.25 , 5.6.1.27
openblas0.2.19
opencv3.3.1 , 4.1.0
openjpeg2.2.0
openmpi2.0.1 , 2.0.1_gcc-4.8.5 , 3.1.0 , 4.0.3
openslide3.4.1
pandoc2.1.1
pango1.40.3
perl5.24.0 , 5.30.0
picard2.8.0
pigz2.3.4
pixman0.34.0
plink1.07
plink21.90 , 2.0
plinkseq0.10
postgresql9.6
primer32.3.7
protobuf2.5.0
pycairo1.15.1
pyodbc4.0.23
python2.7.12 , 2.7.12-ucs4 , 3.6.0 , 3.7.4
pytorch-caffe2.0
qctool2.0.8
qualimap2.2.1
queue3.7
R3.2.5 , 3.3.3 , 3.4.1 , 3.4.1-extra , 3.5.1 , 3.5.1-extra , 3.6.1 , 4.0.1
rcbio1.0 , 1.1
relion1.4 , 2.0 , 3.0.5 , 3.0.5-gpu
rsem1.3.0
rseqc2.6.4
salmon1.2.1
sambamba0.7.1
samtools0.1.19 , 1.10 , 1.3.1 , 1.9
sbgridlatest
settarg7.5.17
skewer0.2.2
slurm-drmaa1.1.1
smrtlink9.0.0
snakemake3.12.0
snpEff3.6 , 4.3g
spark2.3.1
sratoolkit2.10.5 , 2.10.7 , 2.8.1 , 2.9.0
star2.5.2b , 2.5.4a , 2.7.0a , 2.7.0f , 2.7.3a
stitcher0.4.3
stringtie1.3.3b
subread1.5.1 , 1.6.0 , 1.6.2 , 2.0.0
symphony5.6.16
texinfo6.3
texlive2007
tiff4.0.7
tophat2.1.0 , 2.1.1
trimgalore0.4.5
trimmomatic0.36
ucsc-tools363
udunits2.2.26
unixODBC2.3.6
vcflib1.0.0-rc0
vcftools0.1.15 , 0.1.16
velvet1.2.10
vt0.577
xz5.2.3
zeromq4.2.5

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