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Building from source : configure options explained
Packages ngs-sdk , ncbi-vdb , sra-tools have some unusual configure options.
Here we will try to explain them.
ncbi-vdb package depends on ngs-sdk , sra-tools – on ngs-sdk and ncbi-vdb .
ncbi-vdb should be able to find include files of ngs-sdk , sra-tools – ngs-sdk package and sources and build results of ncbi-vdb .
By default build output / build results of ngs / ncbi-vdb / sra-tools is created in
You can change it by using –build-prefix , but then – you should tell sra-tools where to find build results of ncbi-vdb .
Defaults: Standard / default / recommended location of source files
Default recommended locations of source files of ngs / ncbi-vdb / sra-tools is:
ngs / ncbi-vdb / sra-tools packages should be located in subdirectories named ngs , ncbi-vdb , sra-tools inside of the same directory.
Usually it is done automatically by running: git clone https://github.com/ncbi/ngs.git ; git clone https://github.com/ncbi/ncbi-vdb.git ; git clone https://github.com/ncbi/sra-tools.git
Then you should see the following:
If you create repositories as described above and run ./configure and make in each of ngs / ncbi-vdb / sra-tools subdirectories – each of them should find all required files from ngs / ncbi-vdb .
Non-standard location of ngs-sdk / ncbi-vdb
If location of ngs-sdk / ncbi-vdb or their build output directory is not standard (see above), you need to specify it:
- ngs-sdk is in
ncbi-vdb is in
ncbi-vdb/configure requires to find header files of ngs-sdk :
sra-tools needs to find ngs-sdk package and ncbi-vdb ‘s sources and build results.
Configure options are sticky!
Configure options are sticky. Running configure without options will use the options that you used the last time.
./configure –with-debug # will configure with debug
If next time you run
./configure # it will use the same options ( same as ./configure –with-debug)
To clear the saved options and all generated files run “./configure –clear”.
To check current configuration information and options you used run:
Standard option – Install machine-independent data file’s in subdirectories of directory.
Examples of subdirectories are: bin include lib64 lib32 share
Some tools and libraries depend on third party libraries and development headers ( libxml2 , libhdf5 , . ). By default configure will attempt to utilize them from your system if they can be located.
You can provide their location by specifying one of the options: –with-hdf5-prefix , –with-xml2-prefix , etc.
| Brassica napus
Rapeseed (Brassica napus), also known as rape, oilseed rape, rapa, rapaseed and (in the case of one particular group of cultivars) canola, is a bright yellow flowering member of the family Brassicaceae (mustard or cabbage family). The name is derived from the Latin for turnip, rāpum or rāpa, and is first recorded in English at the end of the 14th century. Older writers usually distinguished the turnip and rape by the adjectives round and long(-rooted) respectively.  See also Brassica napobrassica, which may be considered a variety of Brassica napus. Some botanists include the closely related Brassica campestris within B. napus. (See Triangle of U)
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Cultivation and uses
Rapeseed is grown for the production of animal feed, vegetable oil for human consumption, and biodiesel; leading producers include the European Union, Canada, the United States, Australia, China and India. In India, it is grown on 13% of cropped land. According to the United States Department of Agriculture, rapeseed was the third leading source of vegetable oil in the world in 2000, after soybean and oil palm, and also the world’s second leading source of protein meal, although only one-fifth of the production of the leading soybean meal. World production is growing rapidly, with FAO reporting that 36 million tonnes of rapeseed was produced in the 2003-4 season, and 46 million tonnes in 2004-5. In Europe, rapeseed is primarily cultivated for animal feed  (due to its very high lipid and medium protein content  ), and is a leading option for Europeans to avoid importation of GMO products  . Natural rapeseed oil contains erucic acid, which is mildly toxic to humans in large doses but is used as a food additive in smaller doses. Canola, originally a syncopated form of the abbreviation “Can.O., L-A.” (Canadian Oilseed, Low-Acid) that was used by the Manitoba government to label the seed during its experimental stages, is now a tradename for low erucic acid rapeseed that is sometimes mis-applied to other varieties  .
The rapeseed is the valuable, harvested component of the crop. The crop is also grown as a winter-cover crop. It provides good coverage of the soil in winter, and limits nitrogen run-off. The plant is ploughed back in the soil or used as bedding. On some ecological or organic operations, livestock such as sheep or cattle are allowed to graze on the plants.
Processing of rapeseed for oil production provides rapeseed animal meal as a by-product. The by-product is a high-protein animal feed, competitive with soya  . The feed is mostly employed for cattle feeding, but also for pigs and chickens (though less valuable for these). The meal has a very low content of the glucosinolates responsible for metabolism disruption in cattle and pigs  . Rapeseed “oil cake” is also used as a fertilizer in China, and may be used for ornamentals, such as Bonsai, as well.
Rapeseed leaves and stems are also edible, similar to those of the related bok choy or kale. Some varieties of rapeseed (called 油菜, yóu cài, lit. “oil vegetable” in Chinese; yau choy in Cantonese; cải dầu in Vietnamese; and 菜の花, nanohana in Japanese) are sold as greens, primarily in Asian groceries.
Rapeseed is a heavy nectar producer, and honeybees produce a light colored, but peppery honey from it. It must be extracted immediately after processing is finished, as it will quickly granulate in the honeycomb and will be impossible to extract. The honey is usually blended with milder honeys, if used for table use, or sold as bakery grade. Rapeseed growers contract with beekeepers for the pollination of the crop.
Canola oil (or rapeseed oil) contains both omega-6 and omega-3 fatty acids in a ratio of 2:1 and is second only to flax oil in omega-3 fatty acid. It is one of the most heart-healthy oils and has been reported to reduce cholesterol levels, lower serum tryglyceride levels, and keep platelets from sticking together. Some UK farmers (such as Hillfarm Oils) & Farrington Oils) have started to produce cold-pressed rapeseed oil as a versatile cooking oil and dressing, similar in use to olive oil.
Rapeseed oil is used in the manufacture of biodiesel for powering motor vehicles. Biodiesel may be used in pure form in newer engines without engine damage, and is frequently combined with standard diesel in ratios varying from 2% to 20% biodiesel. Formerly, due to the costs of growing, crushing, and refining rapeseed biodiesel, rapeseed derived biodiesel cost more to produce than standard diesel fuel. Prices of rapeseed oil are at very high levels presently (start November 05) due to increased demand on rapeseed oil for this purpose. Rapeseed oil is the preferred oil stock for biodiesel production in most of Europe, partly because rapeseed produces more oil per unit of land area as compared to other oil sources, such as soy beans.
Rapeseed and health
Rapeseed has been linked with adverse effects in asthma and hay fever sufferers.  Some suggest that oilseed pollen is the cause of increased breathing difficulties.  This is unlikely however  , as rapeseed is an entomophilous crop, with pollen transfer primarily by insects. Others suggest that it is the inhalation of oilseed rape dust that causes this  , and that allergies to the pollen are relatively rare.  There may also be another effect at work; since rapeseed in flower has a distinctive and pungent smell, hay fever sufferers may wrongly jump to the conclusion that it is the rapeseed that is to blame simply because they can smell it.  An alternative explanation may be that it is simply the sheer volume of rapeseed pollen in the air around farmland which triggers an allergic reaction in hayfever sufferers on inhalation, or following prolonged exposure to high levels.
The Monsanto Company has genetically engineered new cultivars of rapeseed that are resistant to the effects of its herbicide Roundup. They have been vigorously prosecuting farmers found to have the Roundup Ready gene in Canola in their fields without paying a license fee  . These farmers have claimed the Roundup Ready gene was blown into their fields and crossed with unaltered Canola  . Other farmers claim that after spraying Roundup in non-Canola fields to kill weeds before planting, Roundup Ready volunteers are left behind, causing extra expense to rid their fields of the weeds  .
In a closely followed legal battle, the Supreme Court of Canada found in favor of Monsanto’s patent infringement claim for illegal growing of Roundup Ready in its 2004 ruling on Monsanto Canada Inc. v. Schmeiser. The case garnered international controversy as a court-sanctioned legitimation for the global patent protection of genetically modified crops  .
Worldwide production of rapeseed (including canola) rose to 46.4 million metric tons in 2005, the highest recorded total (source: FAO).
Rapeseed Options Explained
Please ask questions or offer corrections and suggestions. Thanks.
device name: [EDID Product Name] A name for the display (customizable).
device type: [unknown] Sets the icon for the display. When set to projector the ‘screen config’ section is available.
EDID information, some displays are detected with different identifications depending on how they are attached or detected. You can drag and drop these identification entries to combine displays.
the display expects the following RGB output levels: [PC levels (0-255)] This is what your display expects to receive. ‘PC levels (0-255)’ means “use a 16-235 YCbCr to 0-255 RGB conversion matrix” and ‘TV levels (16-235)’ means “use a 0-255 YCbCr to 0-255 RGB conversion matrix”. If the source is flagged full range either a 0-255 YCbCr to 0-255 RGB or a 0-255 YCbCr to 16-235 RGB conversion matrix is used instead.
the native display bitdepth is: [8 bit] This is the bit depth madVR will dither to. madVR offers very high quality dithering so if you are using a low bit depth display (e.g. a 6-bit TN) you may get better quality when setting this to 6-bit. Due to limited support for high bit depths, madVR dithers to 8-bit even when this is set to 9 or 10-bit except when using D3D11 ‘full screen exclusive’ (or D3D11 fullscreen windowed in Windows 10 with AMD or Nvidia GPUs). It can be interesting to turn this down to a very low value (2-4) while testing the dithering options but make sure to have the ‘trade quality for performance’ option ‘don’t use linear light for dithering’ unchecked even if you leave it checked for normal use.
3D format: [auto, disabled] Set the 3D format to: auto, side-by-side, top-and-bottom, row alternative, or column alternative. There is also an option to swap the left and right eyes.
calibration [disable calibration controls for this display]
disable calibration controls for this display: The display is assumed to have a BT.709 gamut with a pure power gamma of 2.2 (probably).
this display is already calibrated: [BT.709, pure power curve, 2.20] This sets the current display characteristics. The gamut option affects the conversions used by madVR when playing video with different gamuts. The gamma options only have an effect when using ‘tone map HDR using pixel shaders’ for HDR content or when using the ‘enable gamma processing’ option in ‘color & gamma’.
calibrate this display by using yCMS: yCMS offers a simple gamut and gamma calibration method. It requires a few measurements of the display that can be done with HCFR. If gamut or grayscale measurements are not supplied only the other correction is performed. Usually bad results (mostly banding and odd effects in shadows) are obtained if gamma measurements below
20% IRE are used so only enter values above 15-30% IRE.
calibrate this display by using external 3DLUT files: Use a calibration package such as Argyllcms, Calman, or LightSpace to generate a 256x256x256 3DLUT to perform a full calibration. For Argyllcms see this AVS Forum thread, for Calman, or for LightSpace. If the provided 3DLUT file contains calibration curves (e.g. in the case of ArgyllCMS, the collink “-a” or “-H” options were used), madVR will load the calibration curves into the system-wide GPU hardware gamma ramps, which affects everything displayed, not only madVR. madVR will restore the original gamma ramps (if any) when it is closed.
disable GPU gamma ramps: [Disabled] Clears system-wide GPU gamma ramps (monitor calibration), if any, replacing them with linear (no-op) curves. This affects everything displayed, not only madVR. madVR will restore the original GPU gamma ramps (if any) when it is closed. This option changes its behavior when using the ‘rendering -> general settings’ option ‘enable windowed overlay’ to only apply to madVR because madVR is emulating the gamma ramps in that case. This option has no effect if a 3DLUT file that contains calibration curves is loaded (see above).
display modes [None]
Allows setting refresh rate and resolution automatically depending on the source video.
list all display modes madVR may switch to: An example for a modern 4K display: 2160p23, 2160p24, 2160p25, 2160p29, 2160p30, 2160p50, 2160p59, 2160p60
treat 25p movies as 24p (requires Reclock or VideoClock): [Disabled] Uses 24 Hz modes to display 25 fps content, it requires Reclock or VideoClock to slow down the audio to match.
hack Direct3D to make 24.000Hz and 60.000Hz work: [Disabled] A hack to Direct3D that enables true 24 and 60 Hz display modes in Windows 8.1 or 10 which are usually locked to 23.976 Hz and 59.940 Hz. May cause presentation queues to not fill.
A second tab in display modes. Allows configuring custom refresh rates and can assist in optimizing them for the purpose of avoiding dropped or repeated frames without frame blending (smooth motion) or resampling the audio (ReClock, VideoClock). Only custom timings can be optimized but simply editing a mode and applying the “EDID / CTA” timing parameters creates a custom mode, and is the recommended way to start optimizing a refresh rate. New timing parameters must be tested before they can be applied. Delete replaces the add button when selecting a custom mode. It uses each of GPU vendor’s private APIs to add these modes and does not work with EDID override methods like CRU; supports AMD, Intel, and Nvidia GPUs. With Nvidia these custom modes can only be set to 8-bit.
color & gamma [Disabled]
pure power curve: [Default] use the standard pure power gamma function
BT.709/601 curve: Use the inverse of a meant for camera gamma function. It has a linear section near black so shadows lighten faster as you move away from black. This can be helpful if your display has crushed shadows.
2.20, 2.40, etc.: [2.20] changes the display’s gamma, based on the display’s settings in ‘calibration’, to this target gamma. Lower brightens mid range values which can be nice in a brightly lit room. Higher darkens mid range values which might look better in a darker room.
hdr [let madVR decide]
let madVR decide: Sends HDR data to displays capable of HDR, otherwise coverts to SDR using pixel shader math.
passthrough HDR to display: Passes the HDR video to the display as is, along with the metadata if ‘send HDR metadata to the display’ is enabled.
tone map HDR using pixel shaders: Enables the options below-
-target peak nits:  Set the target display’s peak white brightness. Above this value is used as the highlights. A lower setting increases the brightness of mid range values.
-tone mapping curve: [BT.2390] The curve used when compressing the range.
-color tweaks for fire & explosions:: [balanced] Keeps the color approximately the same while de-saturating and/or reducing luminance to bring a pixel to a value the display can represent.
-highlight recovery strength: [None] Sharpening the highlights after range compression.
-measure each frame’s peak luminance: [Disabled] Allows madVR to only compress highlights as much as necessary on a per frame basis resulting in more detail in highlights.
-output video in HDR format: [Disabled] Add HDR metadata to the output video.
convert or process HDR content by using an external 3DLUT: Requires display calibration hardware and software. Possible with DisplayCal (Argyllcms) or Lightspace.
screen config [Disabled]
This section is hidden unless the device is set as a projector.
define visible screen area by cropping masked borders: Allows scaling to a smaller resolution and adding black pixels to the edges. Useful if the projector is overshooting the edges of the screen. Only active when full screen.
activate lens memory number: Sends a command to a JVC or Sony projector to activate an on-projector lens memory number.
anamorphic lens: Allows output to non-square pixels.
if in doubt, activate deinterlacing: [Disabled] deinterlace video not flagged as progressive
if in doubt, deactivate deinterlacing: [Enabled] deinterlace video flagged as interlaced
force film mode: [Disabled] force IVTC, reconstructing the original progressive frames from video encoded as interlaced, decimating duplicate frames if necessary. madVR’s IVTC is not functional when using DXVA2 or D3D11 native GPU decoding because madVR’s IVTC algorithm runs on the CPU and the decoded video data is never copied to system memory.
force video mode: [Disabled]force DXVA deinterlacing, uses the GPU’s native deinterlacing. This is the same as automatic and cannot decimate frames.
only look at pixels in the frame center: [Enabled] As described; good for broadcast (with its messy edges) but bad for Anime.
reduce banding artifacts: [Disabled, low/high] Fade detection does not run if both options are set to the same value for a small increase in performance. Five frames are removed from madVR’s rendering buffer every time a fade is detected if the trade quality for performance option ‘don’t rerender frames when fade in/out is detected’ is disabled.
reduce ringing artifacts: [Disabled] Attempts to reduce any ringing/halos present in the source caused by downscaling or sharpening before madVR, e.g. during mastering.
reduce compression artifacts: [Disabled] A deblocking and deringing algorithm. high quality is more significant at higher strengths and is much slower. Chroma often has artifacts but they are usually less obvious and it takes a lot of power to process the chroma channels too.
activate only if it comes for free (as part of NGU): [Disabled] Only runs RCA if it can be run as part of NGU image upscaling. Requires NGU Sharp high for medium quality and NGU Sharp very high for high quality.
reduce random noise: [Disabled] A denoising or grain reduction algorithm. Chroma often has less random noise than the luma.
image enhancements [Disabled]
These are applied before scaling. See ‘upscaling refinement’
disable scaling if image size changes by only: [Enabled, . 2 lines or less] If the resolution needs scaling by the number of pixels set or less no image scaling is done, black pixels are added to the right and/or bottom edge instead.
move subtitles: [Enabled, . to bottom of the screen/window] Move subtitles, this is important when removing black bars or subtitles can be displayed outside the visible screen area. Cannot move PGS subtitles if they are encoded as fullscreen images or Advanced Substation Alpha (ASS) subtitles which have a specific location defined.
automatically detect hard coded black bars: [Disabled] This enables the options below. madVR can detect and remove black bars on all sides of the video. Black bars cannot be detected when using DXVA2 or D3D11 Native decoding.
if black bars change pick one zoom factor: [Disabled, . which doesn’t lose any image content] Using this setting madVR will avoid changing the zoom or crop. e.g. It will not zoom or crop a 16:9 section in a normally 4:3 film when set to “which doesn’t lose any image content” and will zoom or crop all of the 4:3 footage the amount needed to remove the black bars from any 16:9 sections when set to “which doesn’t show any black bars”.
if black bars change quickly back and forth: [Disabled, . once every 2 sec] If not using the above option this option allows a limit on how often madVR can change the zoom or crop while playing to remove black bars as they are detected. Without either of these options madVR will always change the crop or zoom to only remove the black bars.
notify media player about cropped black bars: [Disabled, . no more than once every 2 sec] How often to notify the media player of changes in the black bars. Some media players use this information to resize the window.
always shift the image: [Disabled, . to the top of the screen] This allows setting whether the top or bottom of the video is cropped when zooming.
keep bars visible if they contain subtitles: [Disabled, . forever] Disables zooming or cropping any black bar in which subtitles are detected. Either forever or for a set time.
cleanup image borders by cropping: [Disabled, . 1 line from all black bar borders] Crop extra non-black pixels away from black bars or all edges. When set to crop all edges they are cropped even when no black bars are detected.
if there are big black bars: [Disabled, . reduce bar size by 25%] Allows setting separate handling of large black bars.
zoom small black bars away: [Disabled] This zooms into the video to remove the black bars, cropping a small amount of video off of one edge to maintain the original aspect ratio and resizing to the original display resolution. e.g. The bottom is cropped when cropping small black bars on the left and right and the video scaled to the original resolution.
crop black bars: [Disabled] This crops black bars, changing the display aspect ratio and resolution. Cropping black bars increases performance; the pixels no longer need to be processed. Profile rules referencing resolution will use the after crop resolution.
|16th February 2020, 04:39||#2 | Link|